I have some things that are a little annoying and not sure if they affect everyone or just something specific to my setup.
 
I have a project that is always marked as dirty/changed. I save it and it immediately comes back as having been changed.
 
I changed the instrument icons for the console and track views. Initially they looked great but whenever that template loads, the icons are dithered, the icon pics have soap rings around them instead of being completely transparent.
 
I undocked the browser window and the project will save the position of the window but not the size.
 
Any ideas on these?  No big deal as they are 'one-offs' but the browser window sizing is really irritating.

Re. dirty projects.
 
Some plug-ins seem to trigger this: I assume they have an internal LFO or similar whose state is stored in the VST's instance data, which tells SONAR that something has changed.  It's technically probably correct but is irritating :-)

DrLumen
I changed the instrument icons for the console and track views. Initially they looked great but whenever that template loads, the icons are dithered, the icon pics have soap rings around them instead of being completely transparent.

There's an epic thread on the subject here. No one ever really found an answer, but it seems to happen with only some setups. The most reasonable explanations presented in the thread seem to be:
 
Cakewalk changed the icon code a few times and older icons may be an issue. I guess the fix would be to open the icon and re-save as a 96 x 96 BMP and see if that helps. I've only had this problem occur once and it was in an older project, so this seems like it might be the source of the problem.
 
It could be some kind of graphics driver issue, but who knows.
 
If it's a SONAR issue, I kind of lean toward the theory is that somehow, SONAR grabs the smaller icon when it's supposed to grab the bigger icon.