Try making another folder, add that folder to your auto-import configuration, put the new files there, and see whether it works or not. If it works, add more files and try auto-import again.
Since you are using external hard drive, chances are you have a NTSF partition on the external hard drive, so please check whether you have the most updated version of TuxeraNTSF (i.e. version 2014). Sometimes NTSF partitions play funny tricks on OS X, especially when you use Parallels.
Good luck, and please let us know how it goes.
Best regards,
Y. G.