seraphim,
Sorry about that, but I believe I was mistaken as it doesn't sound just right.
You are right, you should have more than 0.01 amps when charging. Besides, the Trimetric only reads in 10th's of an amp, not 100th's. Is it possible that you have the wrong shunt resistor? Without shore power connected, try turning on one incandescent 12 volt light bulb, the current (negative to indicate out of the battery)should increase by about 1.2 amps.
Also, you may want to set P1 to ~13.5 volts.
Again, you may be best served by contacting Bogart Engineering directly to verify correct setup.
Steve