Trying to use the PS3 Eye cameras at 60 FPS at 640x480 resolution in YUY2 format causes them to drop 50%+ frames and be unusable, but it works at 30 FPS or 60 FPS @ 320x240 resolution. I am using iPi Recorder 1.x.

Is this a known issue - just too much bandwidth or issues with bulk sending of data?

Do you mean that issue is only when recording in YUY2 format, and Bayer format at 640x480@60 is OK?
If so, than yes, it is likely a bandwidth issue - either with USB or with HDD. Bayer format is less space consuming.