My Thoughts
I was the king of transponder issues for a while. I found two things.
1) I had a bad connector in my transponder antenna lead - it allowed my transponder to receive signals (blink) but it would not send the signal out. I replaced the connector and it was all good again.
2) I got a tip that the ignition system would cause issues (constant replying) with the transponder due to noise it kicks off. I use EI and auto plugs and my transponder goes a bit nuts if the nubs on the top of the plugs are not screwed on tight, or if the leads are not snapped on tightly.
Good luck.
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Cheers,
Pete
Amateur Plane - RV-9A N789PH - 2350+ Hrs
Amateur Radio - KD0CVN
Doggies Delivered - 25+
St. Paul, MN
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