I have same behavior with naming on TF.  This is definitely a bummer and a bug.  Most of my presets are custom so reinitializing is not an option.  As with you, each time I save to disk and rename, I get random numbers on TF instead of names.  If you name on TF (a huge pain!) and upload and save, you're OK.  If you do it in FactorLib and download, no names.

Another issue is that, when backing up presets, bank comes out of TF with 1st 10 presets identical, labeled "Preset 1:1".  After this, 100 presets as expected.  But, even when you delete these 1st 10, the same thing happens over & over.  They always come back when loading to FactorLib from TF.  Clearly, there are still some bugs here.  The good news is that the patches are working correctly.  It is just the names that are messed up.  I am attacking MF next.