I have an issue whereby if I use automation lanes for midi info (CC1, CC11, etc), everything works as expected within Sonar on playback, etc but when rendering, bouncing or freezing, the midi info in the automation lane is ignored. I'm using "real time" for render/bounce/freeze to eliminate any issue with the program not being able to keep up.
 
I've done this with both Hollywood Strings and Omnisphere but I'll reference HS for this purpose. Starting with an empty project, I create a new instance of Play and load up any articulation (say one of the Sustain violins). The audio and midi tracks are automatically created during that process. I record a series of notes. I create two automation lanes, one for CC1, another for CC11. I make something like a sine wave envelope in both, anything to generate CC1 and CC11 midi data. On playback I hear what I expect... CC1 controlling vibrato and CC11 controlling expression.

When I render, bounce, or freeze the track, Sonar ignores the automation lanes and the audio file is rendered, bounced, frozen without any of the results from the midi data in the automation lanes (no change in vibrato though CC1 and no change in expression in CC11).
 
I'm on the latest version of Sonar X2. 64 bit Win7 with the latest updates. My soundcard is an Audiophile 2496 set to appox 11ms buffer (it could be lower but it's liberally set to avoid any pops and hiccups and such) with the latest driver updates. Both HS and Omnisphere have the latest updates. Since the problem happened with both of those programs, I have to assume it's a Sonar problem. I just haven't tried it with a third program, I just used those as examples. 

So... does this happen to anyone else?

I think there is a bounce to tracks option to include or ignore automation. Is it checked?

There are several check boxes in the Bounce To Track(s) function that deal with including/excluding automation.
 
I have not experienced your issues myself, and will try to do some research on your behalf in prior threads, but perhaps as posted above you can review the option check boxes to see what you have checked or not.
 
Bob Bone
 

To the original poster: THANKS for providing the detail on what has been troubling you.  As I said, I will try to do some looking to see if I can find something that helps, 
 
Bob Bone
 

Are these simple instrument tracks?
 
Bob Bone
 
 

I don't know if anything here would help:
 
http://forum.cakewalk.com...g-bounce-m2705414.aspx
http://forum.cakewalk.com...-project-m1008641.aspx
http://forum.cakewalk.com...to-tracks-m994077.aspx
 
I hope I didn't just waste your time, 
 
Bob Bone
 
 

Thanks very much for your reply and links. The first link is more or less my issue although my issue extends to creating an audio file through any process (freezing, bouncing, export). I have all the "automation" checkboxes checked, etc. 
 
I was wondering if anyone would mind trying this themselves just to see if it's reproducable outside of me. I've tried everything I can think of, have done it with multiple virtual instruments, etc. It just seems that there's a (huge) bug where Sonar ignores automation lane midi data when rending an audio file through bouncing, freezing or exporting.

I did get a reply from tech support and it is a reproducible bug. Nothing to do really but wait for a fix and to do my midi CC1, CC11, etc in the midi clip itself. Thanks to Cakewalk support for following up and confirming!

Good to know, thanks for posting.    I usually do add CC's directly in the PRV anyway, but now I know that I probably shouldn't try it at the track level.   

I've seen this behavior in SONAR 8.5, too. Specifically with nonstandard (as opposed to just volume and pan) MIDI automation. In my case, I discovered that - surprisingly - the automation would be read correctly during a fast bounce but not with a slow bounce.