I just kept re-exporting until it worked. It only took 2 or 3 times. About 60 percent worked the first time. RED post production just sucks. Good thing the footage looks so good.
I did not figure it out. I just kept re-exporting the clips that were too short until they were the right length. In some cases I had to re-export 6 or 7 times. Red software/fcp plugin is simply not good enough by a long shot methinks.