I see a different instance of what is probably the same problem as #1 occasionally. I haven't had time to collect enough data to report it though.
I brief, what I see is that when I use "Filename (path)" when tagging on a Recording Rule, I can get a message saying a directory doesn't exist, and that directory is incorrect for the rule. In fact, it seems to be pointed at the Windows System directory, which my recordings certainly never go to! I Skip the file to close the message, and typically get three messages per recording. The result is that three file components of a JTV format recording aren't moved, and the recording is broken and unplayable.
While I haven't collected definitive data, the cause seems to be that the files involved are still in use by MC, and hence locked, so tagging using "Filename (path)" at the end of the recording fails, and the files aren't moved. I think I have seen this happen at the beginning of the recording as well, but I have yet to confirm that.
I suspect that problem #2 is just another variation of problem #1.
The MC F6 (Rename, Move and Copy Files) function can handle a "." in a filename without any problem. For example, I have recordings of "Marvel's Agents of S.H.I.E.L.D" which can be moved without issue. I just tested moving a recording to a new location and back again, and it worked fine. I was moving a JTV format recording, but a TS format recording should also move properly. The red (-) to the left of a file just shows that MC can't find a file in the location that it thinks it is in. Basically a "file not found" indicator. If you had Auto Import turned on and MC set to fix broken links, MC would have removed that entry at some time and then re-imported the actual file from the original location again.
I have certainly noticed that MC just doesn't release files sometimes, leaving then locked. But the issue is so random that I can't reproduce it reliably.
PS: I tried to attach images to illustrate my example above, but I see we still can't attached images due to the recent security breach still being investigated and fixed. Never mind, the above should be clear enough.