New Mac users forum: Just throwing this out there in hopes I'm just thick...

First, open disk utility in the Applications/utilities, and repair permissions. Restart. Kill Sophos scanning program files, this may slow down your computer. You only want to have one AV program or nothing at all. If your disk need repair, this is never something to disregard. Onyx does a SMART check and if you ever fail, it could be a failing hard drive (Jimmy Greystone could throw in his opinion on this). If the computer passes SMART check, chances are this is just software. If you have a bootable disk beside your main one (everyone should have it), like external, boot from it, open Disk Utility again, highlight your main drive and click on "repair disk". Hopefully, it would do it and things would get normal. If it registers directory problem that it cannot deal with, you may need to buy Disk Warrior, a very useful and fairly trouble-free utility that can rebuild the directory. It should also be run either from an external drive or from its DVD. Hope this helps and tell us how it goes.
Another simple thing you might like to do is to create another administrative account and upon boot log into it. If the problems disappear, this would mean this is not a system-wide issue and may be fairly easy to deal with.

if AppleJack fails, should be general issue.

especially the piece about Sophos.
Get rid of it entirely. It does nothing for you and will fail the moment someone actually releases a virus that works on OS X .

Boot Disk repair can only be done if the disk is not used for booting. Boot from the OS X installation disk or from an external with OS X installed. It does not matter too much what version of OS X you boot from.

Sometimes you can "over engineer" in an attempt to fix/prevent things before they happen but at first glance I thought that your setup of IPSec, ClamXAV, Sophos and SMC Fan Drive was a little excessive. That last one doesn't give the Mac Pro a chance to work it's own cooling in the way it was designed. Does the Mac Pro reach excessive temperatures when SMC Fan Drive is disabled?

P

First, if I may, address macnerd's addition: for whatever reason, I can't boot into SUM, so AppleJack won't even initialize...it won't go beyond the gray screen till I release cmd-s and allow it to boot fully...then it boots 'normally'.
Now, as to the programs:
I took the proffered advice and disabled Sophos; it was pretty highly recommended, so I figured it wouldn't hurt, y'know?
As to doing the Boot Disk repair, I followed it (literally) "by the book" with a printout of the instructions from Apple and my OSX disk, and to my knowledge followed the instructions to the letter in 'repairing permissions'. That said, I'd also read that OnyX has been sending out a 'disk needs repair' message in error for some time now, which apparently is a bug to be worked out and not an actual disc issue. I figured this out because I'd 'repaired' the disk and permissions several times in fairly close procession, and had the same message come up at the same point...and the SMART status was always OK. I dunno.
As to the SMC program, I've tried to keep the fan speeds in close harmony so as not to disrupt the cooling flow, as I know the 1st-gen MPs like mine get hotter than the newer ones (at least the RAM does). Before I installed the program, the RAM was running in a range from the low 90's to around 140 or so (F). Now, since the RAM isn't all sitting in a nice row directly in the airflow, I'm assuming that the memory closest to the airflow is coolest, right? After installing the SMC, temps began running in the realm of 78-91F, and it seemed the computer became much crisper & quicker in operation.
I could be reading into it here, but from what I've experienced, I like what the SMC does, and disconnecting it doesn't seem to produce anything other than higher temps, at lease vis-a-vis hanging or SBBOD's.
I do agree with you on the IPSec though...I would think that any software program that acts as a firewall would slow things down. Guess I should shut it off and see what happens there.

You guys are great; thanks for your help, and I'm keeping my eye on this thread for any other ideas/suggestions that might help!!!

I have actually repaired permissions several times (last two times I ran a full OnyX, just to be sure...which I have regularly run every month since I developed the AppleJack issue), and have never had an issue with the SMART test...always passed with flying colors.
I went ahead and disabled the Sophos, which I'd added to CX as it seemed CX wasn't as pro-active in finding potential problems (I'd managed to contract a PC virus that I wanted to destroy before it got passed on down the 'Net, and CX didn't faze it.)
Don't have the $$$ yet to get Disk Warrior, but I will as soon as possible. Guess I'm a bit gun-shy getting that one, as I got Drive Genius 2 to fix things up, and it fixed them so well, I had to take my comptuer to a Mac mechanic to get it to run correctly...it screwed up so many things I vowed not to try anything else like that again (y'know?).
I will try your suggestion about the opening a different account and seeing what happens there; I will post back here when I have a result...and thanks!