ManyManyComplexTableField (MMCTF) doesn't seem to remember which items are checked. The MMCTF grid will show up in the CMS admin interface with check boxes by each item. After checking some items, saving the data item, and reloading it in the admin interface, no check boxes are checked.
Hmm, I would say it would have been solved by now in the trunk version. In my experience, the problem does not always occur, only sometimes. I tried a lot of things, but never got around solving it I'm afraid. It's not a problem clients like, btw... Did you try checking/unchecking in different browsers, on different platforms?