I've been looking at the file, and it is indeed a puzzlement.
There is some good news, however. I don't know why it is happening (perhaps a bug, and maybe John would like to take a look at this, too), but it looks like the Paper-filled rectangle from Hinweise layer on the right of Master Ee is being copied to the left half of the actual document spreads on random layers. The pages that seem to be blank are easy to spot in the Page panel (22, 24, 26 & 32) and you can simply Cmd-Shift click on the rectangles on those pages to override and your text and graphics will be revealed. I'm not immediately picking up any other problems scanning quickly through the pages. For a quick and dirty get it done solution, I think this will work, though I would use the .inx file rather than the .indd for the conversion in CS5.5.
I've looked through the file history, and it is long. This started out in 2007 in CS2 and has gone through updates in CS3 and CS4, and been recovered from crashes at least 4 times (which might have something to do with the strangeness). I also think there are a lot of extraneous unused frames on many of the pages. If it were my project, I'd probably clean it up as much as possible in CS4, even going as far as recreating the master pages in a new document and then going page by page and doing a copy/paste in place of all non-master objects into the new file if you don't want to spend the time to place everythign again from scratch, which in my opinion would be a better idea (I tried moving the pages to a new file, but that didn't make any difference in the CS5.5 conversion). You could also rebuild from Scratch in CS5.5.
