It's because the DrawOpa/DrawXlu properties aren't set up properly. They're what determines which polygons are set to which bone. For example, the "EyeYellowM" could be bone ID 2, and every polygon group attributed to that bone will have the same "BoneIndex", as BrawlBox calls it. If they're all set to 0, then they'll be visible all the time. (Which means that bone edits are not necessary to have a polygon group visible at all times -- all that needs to be done is hex edit the values to be 0 in the DrawOpa/DrawXlu).
Oh yeah, I forgot about that XD Those were always set to 0 in v0.64d, but I fixed that

I was hoping that there was hope in that helping find the problem... D:
RTB and Pikazz, would you mind beta testing the current version of Brawlbox and see if you can find this one little problem?
I haven't been able to find it alone... D:
Oh yes, I ran into that error again.
I used Clean on some animations and saved.
Then later I edited one and tried saving, but I got an error.
This is the error: "The given key was not present in the dictionary"
Something has no name...?
@BlackJax96: Does the new feature that you're installing to brawlbox (mdl0 importing) also reduce the headerlen to 208?
if export is v9, yes
if export is v11, no
I think v10 is no too.
Meh, it depends
Btw, the Peach mod froze the wii at stage select and Flandre doesn't work on Dolphin either.