Sure seems like you should have enough power with 2x12AH batteries.
Yes, breakers can be a culprit as they are basically a tiny resistive
heater coil which, unfortunately, drops a significant voltage (lower
the amp rating, the higher the voltage drop!) - but you say you are
using fuses which is a dead short so zero volts drop. But other
things can cause a drop in voltage like a loose connection or some
corrosion somewhere in the path between battery and avionics.
Transponders can be real power hogs if interrogated frequently as
yours is. One suggestion is to have a separate battery for just the
transponder - and if that battery goes flat, then all the other
avionics will stay running.
As you surmise with your comment about the Becker voltmeter, the best
way to check if there is a true low voltage issue is to measure the
voltage at the avionics and then work backwards towards the battery
thought any connections, bus bars, switches and fuses.
Good luck. And glad you made use of my article.
- John