Check your battery contacts in the door and down inside the camera and make sure they are clean...
Many of the Canon P&S cameras have reported problems with poor connections and the battery doors... Clean them (and the battery ends--a clean pencil eraser does OK--just slightly abrasive), and a few people have bent the camera contacts to give a bit more pressure successfully.
Is is possible the Canon "battery door" issue has been exacerbated by opening and closing the door more often as you were working to get CHDK running...
Lastly, of course, it is possible that you have a bad battery...
There is nothing that CHDK can do to cause this problem--especially if you have a clean card without CHDK installed (in my humble opinion--I always could be proved wrong).
-Bill