Animation Render Settings crash After Effects

Hello all,
We have a strange issue on one of our Mac Pros running After Effects (CS5). Whenever it renders with the Animation render settings, it beach balls and eventually freezes, unless you log out of the user and log back in (in rare occasions, it can only be fixed by restarting). However, when it crashes in this manner it takes forever (10+ minutes)to get back up and running. This is the only time it takes a while to turn on or log in.
However, if we change the render settings to say h.274, everything works fine. I don't think it is because it is running out of resources as the Mac has 32 GB of RAM and the file we were testing on wasn't large (< 1 GB). We've tried rendering it on the network or locally on the machine, but it will freeze either way. It is an issue that is limited to this Mac Pro, so I don't think it is just a bug in the software, considering how it isn't random at all and other machines with the exact same set up have no issue. Normally, I would say we would need to update or reinstall a codec if it were third party, but considering Animation is native to Adobe, I don't think that it is that simple to fix.
What do you guys think? Do you think we need to reinstall After Effects?

That's not actually true. It's native to QuickTime, and we just call the QuickTime system to do all of the encoding.
Well, that is good to know.
Also, we have version 10.2 (603.17) of QuickTime.

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