Permissions break as soon as they're fixed...

Question

Ladies & Gentlemen,
After years of nearly trouble-free operation of my MB, I'm getting all sorts of latency, and, more worrying, occasional "you must restart your computer" messages. I don't know if they're related, but it seems that I've developed some weird permissions problems, too.
First, when I run repair permissions, it does seem to help the latency and reduce application crashes... for a short period.
When I run 'repair permissions', I'm getting lots of permissions and user setting errors in the /Frameworks/JavaVM.framework/ directories. Disk Utility seems to fix them all, except that  /RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAgent is almost always identified as "has been modified and will not be repaired"
If I re-run 'repair permissions' immediately after it's completed, I get almost identical results, telling me that all of the /JavaVM.framework/ user and permission problems (that were presumably fixed 60 seconds prior) are wrong again.
Thinking I might have problems with my (newly replaced) hard drive, I've run 'repair disk' several times and the main partition gets a clean bill of health, each time.
I don't know which of these things have anything to do with the others, but clearly my system is not running very smoothly.
Since this doesn't appear to be a hardware problem (at least, not the HD), I'm wondering about some corruption of the OS, but that's wild speculation on my part.
Any suggestions on how to diagnose / fix this problem?

Answer 1

I am now 48-hours post re-replaced hard drive, and things seem to be working very smoothly.
Given the reliability of contemporary drives, I might have been playing the odds about my problem not being a result of a faulty device, but odds don't tell the whole story.
In the past couple days, no weird latency (other than the self-generated type because I insist on having Photoshop, Word, Excel, Mail, Firefox, Keynote, and Dreamweaver all open at the same time), no application lock-ups, no "you need to reboot" messages... Ahhh, the boring life of a well-behaved computer.
The lessons learned from this little episode:
First and foremost, thank God for backups! TimeCapsule and TimeMachine saved my butt three times this past week, turning what would otherwise be protracted downtime and shop-repair into self-manageable fixes.
Trust people with more troubleshooting experience. I'd been mucking about with fixes, command-line attempts to purge a corrupted journal, hoop-jumping to try and re-mount a drive that was destined to fail again. Literally 2 minutes into my description of the problem to the guy at the Genius bar, he told me what the problem most likely was. It took me another 12 hours of (pointless) messing with it to believe him.
Apple stores rock! Apart from the fact that they're the only tech support who don't presume that you're a complete and total moron "have you checked to make sure it's turned on?", they carefully listen to your description of the problem, seek out any weak spots in your diagnosis, then jump to the appropriate corrective steps. I've never felt as though they're starting me at 'page 1' of the troubleshooting manual, to dutifully go through the next 17 steps to arrive at what I said the problem was when I made the appointment. Their staff rocks.
Thank you, Chip, for helping to point me in the right direction so that I wasn't spinning my wheels, trying to solve problems that didn't really exist.