I had the same issue too about 3 or 4 months back. It occured with the same Aperture Library on both my MacBook (2008) and 27" iMac. Around 30k images referenced on Aperture 3.2.x. The number of images I had processing was (nearly) always the same - around 11k images. Number would increase slightly after I imported new images and then stay the same until the next import.
I didn't find any information about others on the forums experiencing this at the time.
I found repairing the database had little effect but rebuilding the database worked on both machines. Once fixed the problem has not reoccurred. I know in your post you said you had tried repairing / rebuilding the database but the rebuild option worked for me.
Good luck and let us know if you find a solution that works for you.