External hard drive frequently ejects itself when using Aperture
A book was just released by SCSC called "Hard Drive Troubleshooting," which mentions disk ejection in numerous places. The book is free and you can get it by going to:

http://www.scsc-online.com

Go to the downloads section and click on the book to download it.

I would think that if the drive is failing over a specific region, the disk will issue I/O errors and MAY timeout causing the system to think the drive is no longer connected. I believe the book mentions something like a 60 second timeout. To me, that would sound either like bad sectors on the drive OR corrupt data on the drive that the system can't make sense of. For example, if your file xyz.dat is either corrupt or unreadable and it just happens to be read by Aperture (and ONLY Aperature) then the problem would occur only when Aperture in use.

If you haven't tried Disk Utility on the drive to verify/repair it, I would do so.

...If you're using Mountain Lion, all bets are off.

Hope this helps.