It seems that the saved conf.ini on Steam overrides the one on your system, so go into the game properties on Steam and disable this syncronisation.
The game reads the conf.ini in your My Documents/1C Softclub folder not the one in your game cache it seems.
I still have’nt got the anti aliasing to work, but running with a properly configured conf.ini has made it playable just !
Its still bloody awful though.