I've seen this too over and over again when using Rename Files from Properties (the old version)
with Autoimport enabled. If you use this tool to move a large number of files on a slow disk (such as a network drive or something similar) it can get all screwed up if the Autoimporter is turned on.
Basically what happens is that the Autoimporter "imports" the new files at the destination before the move operation is complete, and these newly imported files have no tag data associated (of course).
It makes me very angry. My pitiful workaround has been to always remember to turn off Autoimport before I run the tool. If you forget even once though, you can loose tons of data (boo). I posted about this once way back when and suggested that Autoimport be automatically disabled while any file move/copy operation is running (and then auto-re-enabled once they are done).
EDIT: Original report here:
http://yabb.jriver.com/interact/index.php?topic=44053.0Matt, you did respond and made some changes, but I've still seen it happen. Keep in mind that sometimes these move operations (with 100 1GB 720p MKV files for example) can take a LONG, LONG time -- meaning hours, not minutes.