I'm not sure that's it. It's the "export clips" preset, which does seem to use the hardware output. I have 28 tracks in this project. Many are sent to a stereo buss, such as "Vocals", "Instruments", "Drums". I was going to create a video, but didn't have the time. The solution I found was to select all tracks, then using "Control+Click" on the output, set all to "Main Mix". Now when I export all clips, they are fine.
I just checked, and I have no additional sends on any of the affected tracks. It's like because they are being sent to the stereo BUSS before routing to the main out, that the problem occurs.
The routing was simple. Track -> Stereo Buss track (or whatever it's called now) -> Main Out. No additional gain was added, or FX. I triple checked. It seems like a legitimate bug. I'm going to do with with a few projects soon, and will try to create a video showing what's going on.
Note: The only reason I'm doing this is because export to OMF crashes Cakewalk, so this was the next best option.
I've used Cakewalk / SONAR for many MANY years... I'm still a fan (although I've kinda moved on to Cubase - mainly because it's cross-platform).. As a software engineer myself, this is the type of bug I would want to squash!