Check the FMS event log to see if it logs an 'authentication failed' event for when you did the action that connected to the other files.
Also: double-check the file references so that they are all just "file:<some file name>"
I can't seem to see the event log on FM Cloud, but I did make sure that all files are connected with the correct reference.
It seems to be sporadic too...
Very strange, looking for a common denominator.
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You can't see the whole log but you can download it, it's in Subscription > Subscription Center > right-hand pane under "system logs"