Also having the zero kill count problem.
Fresh install of 7.62 into a new folder (C:/Games), patched to 1.06 and the latest version of BSM (w/$100k).
Noticed every skill except for Gunfighting/Hip Shooting can still be raised the old fashioned way. Even wiping out a whole town while hipfiring did nothing.
As long as everything else works, I can live with it, just gotta remember to dump more points into it when starting a new game.