Step 1: Perform a factory reset, then put all the books back on your Kindle without filing them into collections. Report back if everything works as it should.
Step 2: If it does, import the collections from calibre using CM. See if everything works correctly afterwards.
If - and only if - step 1) works smoothly, but step 2) doesn't, then CM might be the culprit... ("might", because it also only uses the underlying Kindle framework functionality. It could just as well be a problem with the framework itself.)