| Hmmm... did you recently install anything of significance? A new application or something?
Mine warns of DVD Player, like yours, and all the Widgets, and Dock, and php... in fact, it's pretty much an exact duplicate of the warnings I get. I can remember this list getting longer and longer through the incremental updates (10.4.1 .. 10.4.5), and most of them pertain to securing holes or vulnerabilities (like the Widget warnings).
If that's the complete list you get when you repair permissions, then all should be well.
The applications crashing certainly doesn't sound right. You may want to first try booting from the Mac OS X Install CD/DVD and run a "Repair Disk" to see if there's anything wrong with the drive. In addition, I would also suggest reinstalling the 10.4.5 Combo Updater -- some people report this helping sometimes.
I don't believe that the crashing and the permissions would be related, but they very well may be.
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