XDCAM Transfer 2.7 still not showing all clips

Shot for the past week using two 8gb cards and two 16gb cards. Have been using ShotPut to offload cards to dump footage to two Lacie Rugged drives and then dumping those at night to a 2 TB RAID 1 Lacie drive.

Clips show up in Clip Viewer and on camera, but only 3/4 of clips show in XDCAM transfer. Thought it was a timecode issue after the first day, so I switched from Clock timecode to Rec Run timecode. Still no use. Clips over two or three minutes show up with proper duration, but no thumbnail and can't be played.

What is wrong with this software? Uninstall and reinstall have had no success either.