Hmm...the tool didn't trim HP Deathly Hallows pt2 even though I told it to, not even one byte, but NDSTokyoTrim took over 4MB off. But the tool did AP fix it, or at least I assume so since it seems to be working on a CycloDS.  I didn't actually bother trying it without the AP fix, what with TC going silent as of late.   It also failed to show the DS-Scene info for that game (error:hash not found), though I assume that's because the game just got released?

One other thing I noticed is that the tool seems to write games directly to the SD very slowly, and I mean VERY slowly.  I end up just saving it to my HDD and then copying it over as that is MUCH faster.

Not complaining or anything, just reporting my observations to try and help you work out any bugs.  I really like this ROM tool, very nice!