A side effect of using BSA Commander to repack meshes I've PyFFI'd is that it causes the Oblivion.esm to load last. What variable causes this and what program is best to have to change it?
I suspect this is because the date/time stamp of the Oblivion.esm file got changed somehow. Oblivion loads all .esm and .esp's in sequence of their file date/time stamps with the oldest dated file loading first.
There is a free tool for date resetting/ changing file dates, I think it's called "SetFileDate", google for it. I have it at home, I can check later for the exact name. However, in your case, one run of your load order through BOSS and the files should be redated correctly again by BOSS.
I do not use BSA Commander. I do all my BSA unpacking and repacking with OBMM. This works just fine and it does not screw with the file dates of .esm and .esp's.
[haegintobmm]