Stop vim from messing up my indentation on comments

For some reason Vim thinks all of my comments should have all indentation removed. If I add # to the beginning of a line, suddenly all leading whitespace is removed. How can I stop this? I have Janus and NERDtree installed, in case it's relevent, along with copious other personal configurations in my .vimrc, but none that (as far as I know) would cause such behavior.