Final Cut Pro: Edit To Tape via a PCI Express I/O card may drop frames with HD: "In some cases, Final Cut Pro will drop frames when performing an Edit To Tape operation, when the video is in an HD format, and the Edit To Tape operation is performed via a PCI Express I/O card.
If your scenario matches these details, you can avoid the issue by disabling Mirror on Desktop while performing the Edit To Tape operation.