It's doing it again. I select a clip in a completely different track to mute/unmute/tweak/etc and it randomly selects clips all over the place thus applying the function I want to perform on the original clip to ALL of them. This is driving me crazy. Is anyone else experiencing this?

Are they in a clip group? When selecting a grouped clip, other clips become selected.  
http://www.cakewalk.com/Documentation/default.aspx?Doc=SONAR%20X2&Lang=EN&Req=Arranging.22.html

Well I just kind of figured out a way to fix it but it makes absolutely no sense to me why it was causing this problem in the first place. In the right click menu I tried "Isolate Clips In Lane" and it kept it from selecting the other bit I didn't want to screw with. But how this started was I was doing something in my guitar tracks (muting a section of a lane) and it muted a section of my MIDI drums. Then when I tried to unmute the MIDI clips it selected unmuted clips so when I unmuted the clips that got randomly muted the ones that WEREN'T muted ended up muted and vice versa. What the heck is going on here?

Anyway... there is obviously something I am missing but that is just screwed up. I tried all sorts of stuff and just happened to hit that isolate clips option on a whim. Does this make any sense? Cheers.

Hi, Bill. I didn't group them or link them at all. At least I didn't intentionally. When this happens when I try to unselect the unwanted clips using the smart tool, ruler, or the blue track select buttons it just reselects them as soon as I try to perform the function (in this case mute). Very strange and frustrating. Is there a global option somewhere to ungroup/link all clips in the project? Cheers.

And to explain a little further while I listen to the whole track to make sure everything is still there... I was working on my rhythm guitar track. I was comping the takes, basically I wanted to mute a section of one take and for some reason it muted my BFD tracks for a section that was in the general area of what I had just muted but it didn't line up to the actual section I just muted. I hadn't even touched the BFD track for ages so it shouldn't have been selected in any way. It's just weird. This was happening as I worked on the BFD track originally too. Random sections were getting selected as I worked with it so as I was trying to delete unwanted takes it would take out other parts with it. Anyway... everything seems okay but I'd like to understand what might be going on here so I can be aware of it in the future.

I should mention I still haven't installed the Quick Fix yet so if it's related to that it might be my own sloth to blame. Cheers.

CTRL+A to select all.  Then right-click a clip and choose "Remove Selected Clips from Groups."

Also, there's a feature that automatically groups clips.  It may be causing the issue.  Check in PREFERENCES > PROJECT > RECORD and uncheck "Group Clips Across Tracks." That may keep this from happening in the future.

Cool, man. I'll do that next time and see what happens. I realize now that in this instance the guitar track I was working on is the first track with events below the BFD track so somehow when I'm selecting the clip I had just cropped and muted it was reaching up into the BFD track and muting the clips in that section as well. At least I THINK that's what's happening. I have no idea how to keep that from happening and I'm a little concerned what's going to happen as move further down my track list. This just wasted a half hour. Ugh. But thanks, Bill. Growing pains or something I guess. Cheers.

I just looked and the Group Clips Across Tracks option was not checked so I don't think it's that. :-/

Were you able to confirm that the clips are grouped?  It would be indidated by a number at the top right of the clips.