Okay, I just shot a new book today, and it should be a good fit for this application -- the book didn't move noticeably from one shot to the next.
I have the pages split into "L" and "R" directories, and specify (via the wizard) the root directory for the source.
The first thing I notice is that the first image in the "R" directory (the front cover of the book) is not recognized. The file should be IMG_6840.jpg in the R directory, but it's not showing up in Book Scan's list.
The second thing I notice is that the second image in the R directory (IMG_6841.jpg) is duplicated 93 times:

- ScreenHunter_01 Jan. 21 14.03.jpg (142.41 KiB) Viewed 1423 times
Then I get the first image from the L directory (also named IMG_6841.jpg) followed by 4 copies of the 3rd image in R (IMG_6842.jpg).
After that, the images start alternating properly between L and R in the list, but the image that's actually displayed doesn't seem to be the image that's selected.
There are several other problems ("R" pages don't rotate, preview and crop doesn't show a cropped image, etc.) but it's my experience that this kind of Java flakiness is usually some underlying problem. The "about" says I'm executing 0.9.5.a, and it's the webstart version.