It happens in the icap/idap package workflow. I would say out of 17 files it happened 4 times. I work on a trade publication where each article is layed out in one indesign file. I then package an icap file and the client then opens up incopy on their machine.

So far the only way I have been able to solve this when it does happen is to place an empty box with a text wrap which blocks the text from droping out from under the original text box.

Unfortunately it is a crude workaround, was hoping for something more efficient.

I am running indesign CS 5.5 and the client has incopy cs 5.5