I actually just realized something about the bots I bought. I have 6 bots, and only 3 were banned. Those 3 were the ones I bought digitally from Blizzard, and the 3 I have from actual box copies are fine. Those 3 that were banned all started off "locked" from the AH until payment processed (had to update their passwords to force it). This patch was fixing something with accounts that upgraded from starter to full, right? And they said they were fixing an issue that could occur there (like permanently being locked out of AH until you update your password). I wonder if that included something that checked those accounts that had already upgraded, and ended up noticing that mine were bots.
Obviously that wouldn't be why everyone got banned in this ban wave, but it could make sense as to why the bans I received were so selective. My first bot, that is the highest paragon and ran the EXACT same setup as one of my banned ones, is still going strong, but he was from a physical copy of the game.