MagickT
I think that I have similar problems when connecting ableton to sonar via rewire. I create a simple loop in ableton drum rack such as 4x4 kick. And sonar chokes every time when I press play button at the loops start. When I try record it to audio in sonar (create audio track and route sound from instrument track with ableton to this audio track) I have similar thing: first kick of recorded loop is corrupt as if 2 DAW do not work synchronously and ableton starting first and sonar recording audio not from beginning.
 
I'm sorry if I made some mistakes. English is not my native language.

I think Sonar generally has an issue with starting playback, in that you'll sometimes hear a glitch as the transport starts. This happens with some plugins as well - for instance I had a problem whereby the first note of a keyboard part (Waves Electric Piano) made a very audible click through one channel when starting playback, and this click even happened when I bounced the audio offline. You could see the click in the waveform. I narrowed the problem down to an instance of SoundToys Decapitator on the track - turned it off and the click disappeared. So I contacted SoundToys and they said it was a new one on them, and then later I tried the same thing in Reaper and found it didn't make the click. 

sharke
I think Sonar generally has an issue with starting playback, in that you'll sometimes hear a glitch as the transport starts.

Remind me again about your audio interface and driver version?
I assume other audio devices are disabled in device manager?

(Here is to hoping my post does not get deleted again by an over zealous moderator trying to single handedly control the narrative).

CakeAlexSHere

sharke
I think Sonar generally has an issue with starting playback, in that you'll sometimes hear a glitch as the transport starts.

Remind me again about your audio interface and driver version?
I assume other audio devices are disabled in device manager?

(Here is to hoping my post does not get deleted again by an over zealous moderator trying to single handedly control the narrative).

It's in my signature - RME Babyface. Driver fully up to date. I don't have onboard audio but I do disable the "AMD high definition audio device" that shows up for my gfx card. 

I also have stuttering on occasions, probably about 1/3rd of the time. Again always just at the start.
 
I've always assumed is something to do with a mis-calculation of plugin latency times that Sonar has to correct after it started, but then again I've seen it with just straight audio files without plugins.
 
The way I work around it is to always start projects on bar 3, using bar 1 & 2 for my count-in. I know I can set the metronome to count in 2 bars, but this way it any potential stuttering is gone before the actual music starts.
 
I admit it's not really a great solution, but it does the trick.
 
M.
 

sharke

CakeAlexSHere

sharke
I think Sonar generally has an issue with starting playback, in that you'll sometimes hear a glitch as the transport starts.

Remind me again about your audio interface and driver version?
I assume other audio devices are disabled in device manager?

(Here is to hoping my post does not get deleted again by an over zealous moderator trying to single handedly control the narrative).

It's in my signature - RME Babyface. Driver fully up to date. I don't have onboard audio but I do disable the "AMD high definition audio device" that shows up for my gfx card. 

Thx. As per usual whatever display mode I'm in on android sig never works on this website.

I have not experienced the issue that you have described, so I am posting this in the sense of some general info regarding a known looping issue with Sonar.  Not intending to troubleshoot your problem, but you may find this info useful.
 
I ran across a looping issue with Sonar and a WaveDNA plugin (Liquid Rhythm) last year, where the vendor indicated a known issue with Sonar and looping. 
 
The plugin can run in standalone mode using its own transport, or as a plugin that is slaved to the transport in the host DAW, such as Sonar.  To loop the Liquid Rhythm plugin, you set a loop region in Sonar's timeline using one or more bars, then hit play.  The plugin will sync together with the DAW and play back whatever patterns you have input in the plugin, and can modify them in real-time as the loop plays back.  You can use the MIDI out from the plugin to trigger another drum kit in the DAW.
 
The weirdness was that sooner or later Liquid Rhythm would just lose the loop sync and stop looping.  Hitting stop, rewind, and play got it working again, but it was annoying...
 
I sent an email to WaveDNA support and received this response:
 

Thank you for supporting our software! I'll do my best to help you sort this out.

Sonar has always posed unique sync issues (like loop region loss, etc). For this purpose exclusively, we have a diagnostic setting I'd like you to try. In Liquid Rhythm, open the Preferences pane and click the Diagnostics tab. Once there, please enable Alternative Playhead Redraw. This was meant to correct the timing between our VST and Sonar. 

Let me know if this resolves your issue. Unfortunately, Bitwig and Sonar have always given us issues. This same plugin version works fine in Ableton, Cubase, Studio One, Logic, Reaper, but is unpredictable in Bitwig and Sonar. I realize this is bummer; I hope you can use our software productively.

sharke
As for PDC affecting things, well I guess there was never any real reason for Sonar not having gapless audio other than the fact that it was never implemented. It's certainly possible...In Sonar I have to stop playback to so much as turn on a send, because if you turn on a send during playback there's a good chance that the audio in the aux will be slightly out of phase until you stop and start again. I think a Baker confirmed that this was a thing some time ago but that they couldn't do anything about it.

When Sonar was born, it was designed as an SUV. When Ableton Live and Studio One were born, they were designed as sports cars. Use the sports car when you want to go fast, and the SUV when you need to carry lots of stuff. Just don't expect to take the corners as fast. 
 
Sonar ain't gonna become a sports car, so what I do is take the corners slower by stopping before I do stuff.

Sharke, when you 'switch off' the VST/Synth do you also turn off all the FX?
I've found that even after freezing tracks, if I don't deselct the fx, they continue to use resources and slow down playback or hinder the CPU. Certain fx are worse than others. If I have two tracks with L-Phase fx, it freezes the system. I can only have one LP-EQ or LP-MB running at any one time, otherwise the CPU doesn't like it. Why this should be, I don't know, but it means that I have to freeze the one track with LP-fx (and deselect all the fx) while tweaking the other 'active' LP-fx. Multiple Izoptope products also take up alot of CPU power.
I don't know if this helps.

Its funny I never got out of the habit of stopping the transport before I do anything to a project. I do this with every DAW I have ever used. I would exempt automation. I have and do write automation while the project is playing back.
 
If I insert any plugin I always stop. Doing any routing I stop. Adding a track or bus I stop.  
 
I also use freeze when I am done with editing a MIDI track and or a synth. 
 
I have been known to mute tracks I no longer want in the mix.
 
 

burgerproduction
Sharke, when you 'switch off' the VST/Synth do you also turn off all the FX?
I've found that even after freezing tracks, if I don't deselct the fx, they continue to use resources and slow down playback or hinder the CPU. Certain fx are worse than others. If I have two tracks with L-Phase fx, it freezes the system. I can only have one LP-EQ or LP-MB running at any one time, otherwise the CPU doesn't like it. Why this should be, I don't know, but it means that I have to freeze the one track with LP-fx (and deselect all the fx) while tweaking the other 'active' LP-fx. Multiple Izoptope products also take up alot of CPU power.
I don't know if this helps.

 
I don't turn off effects (of course, I need them for my mix). The synth is turned off and its audio is printed to a regular audio track, to which I apply effects. If I have a project that's all audio and active synths, I can run an ungodly number of effects in the project and my CPU meters remain relatively calm. I'm aware that certain "lookahead" or linear phase EQ's can cause latency, but I don't generally use those. 
 
So to reiterate, this problem with audio when looping happens with active synths in the rack and has nothing to do with regular FX plugins. And it often happens even when those synths aren't using a whole lot of CPU (which I can see from the CPU activity meter).