Squishy,
what Dave M and i have said,basically you need to look at the source of the problem,that is your Flightplan.
You agree all other flightplans go to the correct folders when converted,but this one doesn't...however when i created it i didn't have any issues that you encountered,so as i said and i repeat it again, you now need to do some work as to why this one particular flightplan wont convert properly.
You may need to speak to Ernie Alston at FS Build to see where it maybe going wrong,see if he as any ideas because i think we have gone as far as we can with this for the time being...