I first have to say that I really like Sonar. I find it to be the easiest to get to know and use out of the others I have and tried. I finally got the time to record a complete song in X3C today. It's really the first time I used it since upgrading. Haven't had much time lately but everything went very well as should be exspected. No issues to report when recording.
 
I had my share of big problems with X2 but I keep chugging on version to version hoping I'd find the holly grail. The things that really bug me are those little things like when I hide my softsynth tracks after bouncing and they keep reappearing in the console view and I have to hide them again and again and again.
Things like this aren't game changers of course but they do get irritating. Every time I switched from console view to track view and back there they were again. So when all those little things pile up in a session it becomes a big thing because you can't concentrate on what your doing. This issue with the hidden track reapearing also happend in X2 and it happens with audio tracks as well. X1 was the most stable version for me. I can't see going backwards though because I like many of the new changes.
Anyway I thought I'd vent a little. I feel better now.

I'm not in front of Sonar right now but could your problem be related to a saved screenset?

Don't forget to sync console view and track view, although that won't necessarily solve all your hiding issues.

It could be that you have a locked screenset, meaning it will return to its original appearance whenever u return to it from a different screenset.

I find exactly the same thing happens to me, on numerous projects.
 
I will go through the routine of making whatever changes I want, including hiding different tracks in Track & Console view (setting is NOT to sync)

1. Unlock Screenset
2. Relock screenset
3. Save project

I can guarantee that whenever I switch screensets, something is visible when it shouldn't be. This is normally in Console View, and this is where Track Manager, for me at least, can get quite flakey.
 
 

1. Hit H. This usually opens up TM, but not always!
2. Then indentify which tracks are showing but shouldn't be. All errant tracks have a checkmark against them. Sometimes, toggling them back off works, sometimes it doesn't. My only workaround when it doesn't is to Close TM, go back into Track View, then Console View, and hit H again.

As an observation, errant tracks are sometimes a complete folders worth, at other times they are single tracks
 
This has been happening to me throughout the X series, and I've switched graphics cards at least 2 or 3 times in the same sort of timescale.

You guys hit the nail on the head. I do have 3 locked screen sets that I use. I unlocked them and tried to make it happen but it just wouldn't happen again... So what am I going to complain about now? Bummer... Thanks guys.