I have Windows XP Pro SP1, using FAT32 fs. I have experienced the same problem (computer crashed, logfiles are truncated with ever-so-much-junk). I am not sure about this, but I think perhaps this is some strange mIRC behavior, and not a problem with crosslinked files.
The reasons for my outrageos assumptions is that when I examine the junk in the logfiles, I tend to find data that was contained in one or more hashtables. This hash table data seems to get dumped first, then a whole bunch of other junk comes following along.
Due to the hash table data (which might as well just be a me-and-my-compy-problem) I would suggest that mIRC simply dumps data from memory into the log file(s) (streams) on a cold reboot/shutdown.
But i'm probably wrong (:
