Just to clarify, it's only the particular program that freezes, not the OS as a whole?
Off the top of my head, I'd say this sounds like a pretty classic case of bad RAM. Pull the side cover off and depending on your model you'll either see a couple of removable trays with the RAM on it, or a single large tray with the CPU and RAM on it. If the computer is running, don't remove either of these things obviously, all you're looking for right now is any red LEDs near the RAM. A perk of the Mac Pro is it uses ECC RAM, which basically has its own built-in error checking. So if there are any red LEDs lit around the RAM, then I'm right, you have either some bad RAM or possibly a bad memory tray. This SHOULD have come up if they ran any kind of memory test on the unit, but let's just say that calling Apple store employees Geniuses isn't just pretentious, it's often false advertising. Just like any other retail outlet, you have a couple of really good people who are surrounded by a bunch of drooling slack-jawed morons that probably can't even find their own rear end with a map.
It would be helpful if you could remember what it is they actually replaced in the past though. Gives us some idea of what they were thinking the problem was. Also if you could figure out what specific model Mac Pro you have that would also be helpful. It sounds like an Early 2008 model from the specs, but I sadly don't get a lot of Mac Pros to play with, so am not as familiar with the different model specs. So if you open the thing up, and look inside, do you see just a single tray with the RAM and CPU on it (there are two push levers on either side of the tray) or do you see two dark blue cards with RAM on them sticking out on the lower right? Some of the older model Mac Pros had recalls on the video cards which could also be part of the problem. So if you have a GeForce 7300GT, Radeon x1900 or Radeon 2600XT, that could definitely help narrow the problem down. You just want to hope it's not the 7300GT, because that program just ended, but I think the other two are still active, so would potentially qualify for a free replacement. You might even be able to convince them to retroactively reverse previous repair charges for being idiots and not looking up if there are any extended repair programs going on with the unit they're working on. Maybe, maybe not, but I'd say it's worth a shot.
MacPro, Quad Core Intel, 3GHz, 4 GB RAM, OS 10.5.8
Working as a graphic artist, I most often use Adobe Photoshop as well as InDesign, and rarely Illustrator, etc. (CS 5). Sometimes I can work for hours, no problem and then applications freeze inexplicably, abruptly. They will not force quit and I cannot restart from the menu bar, and must turn off the power button and back on. I've zapped the PRAM and repaired permissions countless times, and removed all of my many fonts and carefully reloaded them one by one on an as-need basis. I've taken this computer to the Apple Genius Bar 4 times in the last several months, they've run a number of diagnostics and replaced a couple of minor pieces of hardware and say everything should be fine. But still the applications crash (Mail, Photoshop, you name it) and now job files that were saved sometimes become corrupted when I go to reopen them.
Any ideas as to how I can find out WHAT is wrong?