We have finally managed to duplicate and hence understand the problems people have been having with FactorLib and V2.0 presets.
A V2.0 preset has no name. When you send it to V3 software on your pedal, the pedal gets slightly confused, and decides that the name is the start of the next preset, which looks like "[3] 0 2", or similar. If you send it back to FactorLib, this will view this name as a very short preset and carry on loading. As a result, you get the actual presets, preceded by the spurious very short presets "Preset 1.0". Your backed up presets are safe, you just have these spurious naming issues.
To further complicate things, it appears that you can rename your V2 presets on FactorLib, but if you send them to the pedal the new names are lost.
There are two possible work arounds:
1) Rename any presets on your pedal with bad names and save them. You must do the rename on the pedal, not FactorLib. See the TF/MF/PF update page to see how to do this if necessary.
2) Alternatively, send them back up to FactorLib and delete the spurious presets "Preset 1.0". Send them back to your pedal (again), and your original presets will be named "Preset 1:1" etc.
Once you have done either of these, you will have V3 presets with valid names and the problems will not reappear.