When bouncing to tracks on some occasions the bounced track has both noise artifacts, actually it's more like pops and a few notes getting partially cut off.  The timing of some of the notes gets a bit off also, so a few notes will be a half second to early.  Has anyone else experienced this and is there a way to prevent it ?

you can not only have issues related to buffers and rendering during playback but also when bouncing.  Try increasing your card buffers and unticking fast bounce.  There are numerous other computing factors that can affect a bounce as well.

• Turn your midi buffer up. Mine is around 1050.
• If you are using automation, check if you are going to 100% full or 0% on your automation ribbon and try 99% and 1% instead on your automation.
• Turn off your network card in the device manager (disable the ethernet or wifi device, you can turn it on and off at will)
• Disable all auto-protect on anti-virus software. Some also do maintenance tasks which can eat up hard drive or ssd reading cycles.
• Turn off all power management.
• Do not have anything else open that uses the audio card. and disable any other audio devices in your system (AMD HD raedeon sound driver can cause issues, maybe others too). Most usb audio hardware (virus TI, Bassstation 2, Arturia, don't have sharing issues, you should be able to keep them installed).
• If all else fails, ctrl-alt-delete, task manager, user tab, then start ending task on stuff not needed for sonar or the computer to run. If you are unsure about a process, copy the name and google it to see what it does.

 
 

I have to respectfully disagree, and say that most of that isn't relevant to offline rendering;  your audio drivers don't get involved, and hardware interrupts will have no effect, except possibly to increase the time to complete. Likewise, the MIDI Prepare Using buffer only affects real-time playback.
 
Disk-writing errors are a possibility, but, again, offline rendering isn't time-sensitive, so SONAR can wait as long as it takes for a write to complete.
 
My money would be on VSTs that behave badly under fast bouncing and/or when the ASIO buffer is to low, since offline rendering uses that same buffer size for processing by default. If that's the problem, you can either raise the buffer size temporarily, or set a non-zero BounceBufSizeMsec value in AUD.INI. Zero is what tells SONAR to use the ASIO buffer size. I've had this set at 20 (ms) for a long time, and higher values may improve render speed in some cases. The only caveat I know of is that Bitbridged 32-bit synths will have an empty buffer of audio added to the rendered file, so if the buffer is high Bitbridged audio will play late as a result (JBridge doesn't have this issue).
 

Thanks all !
I've already adjusted/turned off all those settings and processes, so it's likely more along the lines of brundlefly (good handle BTW).  I will try some of these adjustments.
 
Also forgot to mention I've been using full bounce (not fast bounce), assumed that was better (higher qualtiy) but not sure if it's an issue.

OK I think I narrowed the problem down a bit.  After bouncing the track I am stretching the clip and changing the key and tat seems to be causing the artifacts and timing changes.  When I listen to the bounced track in the original key it sounds fine.  Any thoughts on minimizing the damage when doing the key change ?

Assuming you're talking about rendering MIDI-driven synths - as I think we all were - it make no sense to change timing or pitch after rendering. Change the MIDI and re-render it; musical editing in the non-audio realm is what MIDI is all about.
 

Transposition is very easy in midi -- time change is not so easy but certainly possible with a calculator.    You've got an initial total duration, and a desired total duration ... use the "shift" dialog to change all midi notes according to desired divided by initial.    ... You want the result to be half again as long:   1.5/1 = 1.5 for the parameter.  You want it 10 percent longer, 1.1/1 = 1.1   You want a duration of 0.877 to be a duration of 0.933?  Use 0.933/.877 in the shift dialog