I have the latest Sonar Platinum (2017.01) and I'm trying to work out some tunes using a Roland TR-09 (Boutique version of the TR-909) drum machine, which is set up to sync with Sonar via MIDI clock. I have MIDI clock enabled on the MIDI port the TR-09 is connected to, and when I hit play, the drum machine runs along perfectly in sync.
 
HOWEVER, when I start recording on Sonar, where I have the Metronome Count-In enabled, when I hear the Count-In click, the drum machine will start playing a little after the 2nd beat. Like this:
 
[Hit Record] ... 1 - 2 [TR-09 starts playing] - 3 - 4  - [SONAR starts recording].
 
The TR-09 starts a few milliseconds after the 2nd beat, so even if I set the Count-In to 2 beats, it would not sync to Sonar when the metronome count-in is enabled. Again, disabling the count-in or playing Sonar will result in the drum machine syncing along normally.
 
I've tried this on another DAW I use (Studio One) and the Count-In sync problem does not occur; the TR-09 syncs normally whether there's a metronome count-in or nor. So it looks like it's isolated to be a Sonar issue.
 
Is there a solution to this, other than not recording with a metronome count-in?
 

by any chance, do you have a tempo change right at where you are starting to record?
 
I remember having issues a while back with count-in (in general) in such a situation...

how are you connecting this machine ?
Is it possible what you are hearing is latency ?

Rob[atSound-Rehab]
by any chance, do you have a tempo change right at where you are starting to record?
 
I remember having issues a while back with count-in (in general) in such a situation...

 
I don't think so; this is a blank template. 
 

chuckebaby
how are you connecting this machine ?
Is it possible what you are hearing is latency ?

I'm connecting it through the MIDI, not USB. 
Latency is ruled out since there is no problem when I'm not using the Metronome Count-In click. The machine starts right on the beat when I don't have the count-in enabled.