FlashGet might get banned soon.. so its better if you move to utorrent...

Try this ,

under the preferences of utorrent... set all 4 directory locations .., ie locations under downloads and others location (both incomplete and complete)... and make sure that location is outside My Documents.., it can be c:\torrent\incomplete and c:\torrent\complete ...

Give it a try and lemme know if it worked.,. ,if doesnt then post screen shot of utorrent error that you get , we will think of something else...

Also , dont set both of them to run at startup ., they will interfere with each others data.