MOONEY PLT EXPERIENCED CONTINUED MODE C PROBS IMMEDIATELY AFTER ANNUAL MAINT CHK.

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ON OCT/WED/03; I PICKED UP MY ACFT AT 3K6 AFTER BEING ANNUALED. PART OF THIS ANNUAL INCLUDED THE PITOT STATIC SYS/XPONDER CHK. THIS 24 MONTH CHK WAS COMPLETED AND THE LOGS WERE SIGNED INDICATING THIS SYS WAS RETURNED TO FLT STATUS. UPON DEPARTING FROM 3K6; AT ABOUT 5000 FT; I CONTACTED ZKC AND REQUESTED FLT FOLLOWING TO LOU AT 9500 FT. SOME TIME AFTER LEVELING OFF AT 9500 FT; ZKC ASKED WHAT ALT I WAS CLBING TO. I ADVISED THAT I WAS LEVEL AT 9500 FT FOR MY FINAL ALT. ZKC ADVISED THAT MY ALT WAS READING 8900 FT. WE TRIED TO RECYCLE THE SYS; BUT STILL WAS READING 600 FT LOW. WHEN ASKED TO CANCEL 'ALT SQUAWK;' I FOUND OUT THAT THE XPONDER HAD A SWITCH PROB AS EVEN IN THE 'ON' POS; WE WERE SQUAWKING ALT. ZKC CANCELED MY RADAR SVC. I THEN CONTACTED EVV APCH AS I WAS NEAR THEIR AIRSPACE. THEY ASSIGNED A CODE AND WHEN RADAR CONTACT WAS ESTABLISHED; ADVISED THAT I WAS READING 9000 FT INSTEAD OF THE 9500 FT THAT I RPTED. I EXPLAINED WHAT HAD TRANSPIRED WITH ZKC AND THE EVV CTLR ADVISED THAT HE COULD PROVIDE RADAR SVC WITH THE INCORRECT 'ALT SQUAWK' AS LONG AS I ADVISED HIM PRIOR TO ANY ALT CHANGES. AFTER XING EVV AIRSPACE; I WAS HANDED OFF TO SDF APCH. I INCURRED THE SAME PROBS WITH SDF. MY SQUAWK INDICATED 500-600 FT BELOW RPTED ALT. AS I WAS DSNDING FROM 9500 FT TO 3500 FT; WE CHKED THE SQUAWKED VERSUS ACTUAL SEVERAL TIMES AND FOUND THE ERROR TO BE CONSISTENTLY 500-600 FT LOWER THAN ACTUAL. I WAS HANDED OFF TO SDF TWR. XING OVER THE NUMBERS OF RWY 17L&R AT SDF AT MY ASSIGNED ALT OF 2500 FT; SDF TWR ADVISED THAT I WAS READING 2100 FT. AS THERE WAS TFC BELOW ON THE APCH TO RWY 17L; TWR WAS CONCERNED AND REQUESTED CONFIRMATION OF ACTUAL ALT A COUPLE OF TIMES. I WAS THEN HANDED OFF TO LOU TWR. ON FINAL FOR RWY 24 AT 1100 FT; I ASKED FOR AN ALT RPTING CHK AND WAS TOLD IT READ 900 FT (200 FT LOW). ON OCT/THU/03; I CONTACTED THE SHOP THAT PERFORMED THE ANNUAL AND WAS ADVISED THAT THE AVIONICS TECH HAD ADVISED THEM THAT THE ENCODER ON MY ACFT 'MAY' BE INTERMITTENT. THIS BIT OF VERY IMPORTANT KNOWLEDGE WAS NOT RELAYED TO ME IN ANY MANNER PRIOR TO PICKING UP MY ACFT. CORRECTIVE ACTIONS: I HAVE ORDERED A NEW ENCODER TO BE INSTALLED IMMEDIATELY. RECOMMENDED ACTIONS: 1) AVIONICS TECHNICIANS SHOULD NOT SIGN OFF THE 24 MONTH PILOT STATIC/XPONDER CHK IF THERE IS A QUESTION ABOUT THE RELIABILITY OF THE ENCODER. 2) THE SHOP DOING THE ANNUAL MUST COMMUNICATE ALL INFO/CONCERNS; ETC; REGARDING THE STATUS OF THE ACFT AND ITS EQUIP TO THE PLT -- PRIOR TO RETURNING THE ACFT TO SVC.