Sorry to kick a dead (well, it will be soon) horse, but quick rundown on the version numbers...
3.90.x is the heavily tweaked versions that are [generally] designed to sound best with the --alt-preset modes. 3.9x are the bone stock ones that have the most cutting edge technology, hence, why they're faster, but also have more bugs, and sometimes, not as good SQ.
I myself use 3.90.3, FWIW.
(-:Stephonovich:-)