After Effects CS6 - Project Files Virused?

Guys,
I'm collaborating on a stereo TV show with several other CG artists (living around the U.S.), and one of them has been complaining for months now about how his AE project files (created with CS6, running under Windows 8 64-bit) have gotten huge, and take literally hours to load. He then shipped us the files for us to examine.
Here's the deal: one of his .AEP files clocks in at 222 megs, and when I loaded it into my copy of CS6 (running on a dual Xeon machine, Windows 7 64-bit, 32G of RAM), it took 45 minutes to load. (Another one of our artists, working on a Power Mac, tried loading a different project created by this guy, and it took 10 hours to load.)
I then proceeded to completely rebuild his comp in my copy of AE CC -- I loaded all his original footage (a combination of 32-bit .EXRs, .PNGs, .TIFs and .TGAs), set up the layers and effects filters exactly like his, and then resaved my file.
Result: my file is 2 megs in size -- 1/100th the size of his file -- and it loads on my machine in 5 seconds.
Has anyone ever heard of something like this? I'm wondering if somehow a virus or Trojan put an enormous amount of spurious data in these files, or if they were somehow created with a cracked version of AE or some other plugin, and our legit copies of AE are brought to a standstill with his bad .AEP files. (Note: I scanned his files and footage with Avast Antivirus, MalwareBytes and the Windows Malicious Software Removal tool, and came up with nothing.)
Here's the other weird thing: I loaded one of his project files, then started deleting layers, footage, and comps, and kept resaving the project and checking the file size. Even after I deleted every single element in the project -- it was completely empty -- and saved it, the file size went down from 222 megs to only 214 (and that empty project file still took 45 minutes to load.) I saved this empty project as an .XML (.aepx) file, and that file is 430 megs!
What in the world is going on here? We really need to figure this out, because it's destroyed our productivity on this show having to rebuild these comps. Thanks,

Guys, all the footage is CG and was rendered from Lightwave -- there was no live-action footage to "camera track" or "stabilize."
Second, most of these comps don't even use a camera inside of AE -- they're 2D comps entirely.
And again, as an experiment, I deleted literally everything in the comp and saved a completely empty project, and the file was still huge and took 45 minutes to load. How can that be?
I would really love to send one of these files to Adobe and have you guys load it into a debug version of AE CS6 to see if you can identify what the problem is. Thanks,

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    If you want ot know more, here's an FAQ on the basics of rendering and exporting in AE...
    http://help.adobe.com/en_US/aftereffects/cs/using/WS3878526689cb91655866c1103a4f2dff7-79f4 a.html#WS3878526689cb91655866c1103a4f2dff7-79f1a

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