I had this same problem with classic apps -- when the TruBluEnvironment (what's behind classic.app) goes down, I see all the dock strangeness that you describe. But never have I seen this with native carbon apps... Nor have I heard of the trash problems you report.
Have you reported this to Apple?
Do these problems go away with a logout and login? Or with a stern restarting?
If not, maybe somehow the carbon frameworks or "LaunchCFMApp," the BSD application that launches carbon apps, got messed up? This should not happen unless the system itself stomped on the files, because user programs shouldn't have the power to do that. If that's the case, a reinstall may be necessary.
Things to try:
1) Open the "Console" application in the Utilities folder (or is it Grab Bag?). Then try to open a carbon app. Look for any messages that pop up in the console while the app tries and fails to start...
A console error message might tell you where the problem is.
2) Open the "process viewer" application. If you can sort by run time, do that, so new apps coms up on top. Otherwise sort by name and scroll to where the "L's" should be. Now try to open a carbon app. Does the name "LaunchCFMApp" show up in the process list at all during the procedure?
I don't know how much knowing if "LaunchCFMApp" starts up would tell us, but it might be a lead, and it might help Apple sort out the problem...
[Edited by zpincus on 12-20-2000 at 01:23 AM]