Well, it could be because the non steam version you downloaded was based on the old CS version and your config was for whatever reason messing up with the settings in the new one. But nothing really changed aside from few cvars here and there.
Well, rates changed among other things. Nowadays you set it to 100000, whereas it was 20000 before. Stuff like that. There is news piece written by lurppis on this site from around that time that goes into details on this.