I'm sure we've talked kernel panics in the past, right? rears its nasty head again? no need to revisit except to say, what's new this time??
Next up: I take it "iDVD contents from Apple" ? Explain.
Disk Utility: don't rely on it. Don't use the version on DVD. Use another disk drive, Ms. "Emergency OS X Only" for doing repairs and has strictly Apple OS and utilities, you know, TechTool and Disk Warrior and gang.
Updating OS X.
Backup. Repair. Wait and read. Check MacFixit and MacIntouch for 3-4 days to wait for feedback (always something to learn). Some people do/will have trouble and I can learn from those, too. Use best update practices.
Only use the combo update. Apple the update after doing backup and repair; and, run the update from your "Emergency" - you can change the target volume to other than the drive you booted from.
Consider cloning OS X and applying the update to your "Test 10.5.5" system volume to insure it works.
I know 3.2GHz is top of the line, bleeding edge, finely tuned, and could be less forgiving of line current coming in (you need a 1500VA UPS at least), also heat and other possible issues. It comes with a higher duty PSU, too.
It isn't behaving, take it in. Intel is always improving their chips. They've managed to reduce power requirement and therefore heat, and safely get 3.4GHz now.
You did do a full clean install 'recently' so you really shouldn't need to do so again. And you should have, right? a backup/clone of your fresh install, so you never have to go through the work again, you can just restore from backup image; and, you have used TimeMachine and SuperDuper to make backup of "/Users" and data as well. So you can restore those.
If AHT gives "pass" or "Okay" and the fans work, and you keep the fans running 900 rpm... weather is still warm and your/our Mac Pro puts out a good deal of heat, so cooling is an issue...
I don't worry about Permission errors, I just run it, BUT, you should NOT run Repair Permissions from the DVD, Apple warns that Leopard you need to use the latest version of Disk Utility, hence, create that "Emergency" system and use that. Also, repair the drive with Disk Warrior, okay? Permissions can always be repaired while booted, it doesn't need to be done from 2nd drive (unless you can't boot of course, in which case you have more serious concerns).
People worry too much about permissions. Needed, do it and forget it and only before/after installing software and updates. It has no magic. Same with resetting PRAM.
Anyway, rerun permissions, and don't use CD/DVD for that anymore, it is a "no-no."
Panics are hardware, usually.
If you are dealing with 10.5.5, read through the last three days of reports on this on MacFixit/Touch - the later is mostly user feedback that is hard to make head or tale, Fixit focuses on troubleshooting fixes and problems aimed at solutions.
http://www.macfixit.com