Hi ChaosPotato, upon immediately deleting all my mods from .25 to get that clean stock .90 beta play through I was hit with the same problem as you, however after a little experimenting in sandbox mode, I figured out that in order to use SAS you have to have a 'Pilot' on-board, as out of the original 3 (Jebadiah, Bill, and Bob) only Jebadiah is a pilot and therefore Bill cannot activate the SAS the same goes for Lemeny, you can check what they specialise in by going into map view and clicking on the 'Crew info' tab on the right, there are 3 roles kerbals can play on your spacecraft, Scientist, Engineer and pilot, unfortunately for you Bill and Lemeny are not a pilot. Hope this helped!! :3 ~ Andy0432