Emptying Aperture trash doesn't remove images from library

Not sure what's going on.
Did a little house cleaning over the past few days and deleted about 2K images overall. And I emptied the aperture trash. The number of files in the program goes down. But the size of the library doesn't change. The date of for the library does change and shows the current time.
I archived all my images to an external vault. That vault is significantly smaller than my library.
Then I upgrade to the new version 3.1.2. Deleted preferences.
I created a new library as a test. I imported 188 images. Then deleted a few. Emptied the aperture trash. The number of images went to 152.
The size of my library remained unchanged. No aperture images in main computer trash can. And when I go into the masters folder in the library I see all 188 images there.
System: mac pro 2006. OS 10.6.8

Thanks for taking the time to reply.
I don't remember which version I upgraded from. But the problem was there in the old version as well as the new one.
I did do the repair rebuild just before upgrading with only a 0.1GB difference in file size afterwards.
And, as I said, when creating a brand new library with only 188 images the same problem occurred. So 2 separate libraries on the same drive.
I just created a new library as a test on my main drive (a different drive) with the same issue. Files are deleted in the program but not in the library.
There is no problem with the trash in any other respects. Other files have been deleting just fine.
The aperture deleted images aren't even reaching the trash can.
I might need to reload aperture.

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Emptying Aperture trash doesn't remove images from library

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