I opened an IDML containing tables (not spanning over several pages) and all the tables were moved vertically to the top and out of the page, so I am only able to see one third of them.
It seems to be that APu is inserting and pinning them into separate text frames and in this document the pinning goes wrong. I made another test in ID cutting the table and inserting it again. This time the table was still pinned into a text frame, but displayed correctly. Why is APu handling the tables not as a table object and instead pins them?
IDML can be uploaded to a private link for examination.