A couple of tests/questions come to mind:
- Are the frame numbers the same in Houdini, that is also negative frames?
- And are the problematic frames and channels displayed in Houdini correctly?
- Do the negative frame numbers show up in the filenames correctly?
- If you load the individual files from a problematic frame into C4D, are the channels missing as well? If so, how about if you load the same individual file into Houdini?