I was having a similar problem with an old Seiki vinyl cutter. I figured it was just something I had to put up with from a cheap cutter with the bundled flexistarter software. What I finally discovered was the problem... the drive belt which controls the material rollers had a small tear in it, just enough to let it stretch a bit beyond its original length. This caused the vinyl to not return to quite the same place when completing cuts. I replaced the belt with one from Bando that seemed a little more durable than the original, and the problem is resolved. Perfect cuts over and over. Sometimes it is not the software, and trying to trick software into fixing a mechanical problem can be difficult to say the least.
Regards