Sudden and odd menu tracking issue

So this morning when I logged in, my menu tracking behavior changed very annoyingly. Normally, when you click on a menu, the menu captures the mouse until the menu is dismissed by selecting an item or clicking outside of it. Now, the menus are behaving more like dialogs in that they are no longer capturing the mouse and I have to click twice on submenus to get them to open. Worse, I can't select sub-menus in context pop-ups the expected way either.
In short, it appers menus just suddenly quit capturing the mouse resulitng in these annoying side effects.
This is system wide. It doesn't matter which user is logged in or which application is running.
Is there a weird setting somewhere my cat might have found?
Yes, I've already done a permission repair and rebooted. I actually did have this happen before, but I'm not going through another OS reinstall for something this stupid.
Mac OS 10.6.8

Ryan,
To make sure that I got your info straight:
The file that you are having problems with was originally a PAL MOV file, that was muxed with with PCM WAV audio. You converted it to NTSC, then de-muxed it to a m2v file with PCM WAV Audio. You added the m2v, the WAV (Audio Track 1) and an AC3 Audio (Audio Track 2) to Encore's Timeline. This is the file that you're having problems with. Is this correct? Is the other file (the one that plays perfectly, on a separate Timeline? Was the PAL -> NTSC conversion done on the muxed MOV file, before you split to elemental streams (Video and Audio)? What is the runtime of the MOV file, 01;38;01;00 (1 hr. 38 min 1 sec 0 frames)? Where did the AC3 come from - re-mix of the PCM WAV in 5.1 maybe? Did this file come after you had converted from PAL to NTSC? The DVD9 of this Project, with the same Assets, has no problems, only the DVD5 of this part of the total, right?
In Encore's Timeline, when you Zoom it in to max., and look at the end of the files, do they all line up perfectly?
First, I want to make sure that I'm reading/understanding the specs. of the Project correctly, and also getting a handle on the operations performed so far. This will also provide others with a schematic of your Project and the workflow to produce it. Maybe someone can see a red flag, and suggest a change, or correction. Depending on the answers, I have a hunch, but don't want to waste your time, tilting at windmills.
Thanks, and good luck,
Hunt

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