Got the plane back, annunciator keeps flasing "MSG!MSG!MSG!" about half the time my MSG button says "Altitude Failed". I've never had a problem with my encoder that I know of. So I picked up FF Friday just to see if they lost my altitude. Well I was getting put through the wash with all the turbulence and they never said much other than gave me a squawk code and "Radar contact lost, squawk VFR, good day" as I was on the edge of their coverage anyway. Coming back today I called them up good and early. They said "Radar contact, 8,500 13NM east of Missoula" After I put in my squawk code, about 3 miles or so later, i get "Cherokee 00W, say altitude", The frequencey wasn't busy so I replied "My GPS is telling me it can't read the encoder", He said, "I had you for a minute but your mode C is INOP, he never had my alt for the rest of the trip (about half an hour in the system). Avionics guy says its a bad encoder (Ack30 or something). I'd never had an issue with it before this avionics work, but I'd never had anything in the plane to let me know but I always get on traffic advisories transitioning over the MSO airspace and for all XC trips that go west and nobody has every said "say altitude" Encoder or something got bumped loose?