I have the same problem with one of my runs. I've never used the scheduled runs feature. I've always just done a quick start outdoor run. On the run in question, I had trouble with the GPS acquiring and signal. It timed out at least once. Once it synced I started the run. About 200 yards in, I got 2 additional audio cues that the GPS signal was acquired. Bizarre, but a quick look at the display showed that it seemed to work normally so I didn't stop.
In addition to that glitch, I didn't start the music on this run like I normally do. Normally, I swipe to the music screen and drill down to my playlist, start the music, back out to the workout screen and drill down to a quick start run.
On this run, I hit the music button and hit play. The type of music I normally run to started so I thought nothing about it, but 5 minutes into the run, a song not in my normal running list played so I swiped to the music page and drilled down to my normal playlist and started it and ran on my sweaty way. I did skip a few songs along the way.
Those are the details around the problematic run I have.
If the workout download is indeed working, it would seem to be a parsing error. My theory is that one of the two events above (the GPS or music problem) is a case of a processing thread not being killed correctly and the device recording two (or more) sets of data associated with the run. Worse case I can imagine in three GPS threads logging data against 2 music threads. If that's the case, I'd check the killing of the threads or recording the PID of the thread (GPS and music) so that can be identified. Heck if that is the problem, my workout would be 60k instead of 10k. Sweet. On the minus side, that means the details of the run are hopelessly garbled and can only be approximated when fixed. Junk, but I don't live and die by my workouts and the split data still appears on the MOTOACTV itself.
Perhaps if there were a way of syncing only the data being displayed on the MOTOACTV's screen. I'd be willing to mark some workouts as needing to be uploaded again (on the portal or the MOTOACTC) and re-syncing the data. If there were a way.....