Back in the olden days of SCSI, compression artifacts that showed up in different spots with each compression run could most likely be blamed on the connections to and pathways from the drives. SCSI cables, terminators, or SCSI card software.
If you cannot get a gut feeling for the likely cause (bad media, bad files, out of spec video levels, bad MPEG4 workflow, I dunno, lots of weird possibilities but you’re the only one who can tell if any of them are likely) you will need to debug your compression workflow.
Try using a shorter clip for your many rounds of tests so you’re not wasting a bunch of time. Export the shorter clip to a different drive and write the compression output to a different drive.
Sorry not to be able to nail it for you. Hope you get better and more specific advice.Iif you have cross-posted in other FCP or Compressor forums, please return to them all and let us know how you fixed this.
bogiesan