Dimitri,
You may have better luck posting this in the RRC-1258 section. This is the Webswitch forum.
I also use two FT-2000's in a YaesuTwin setup. A couple of minor quirks, otherwise ok.
Make sure that the two RRC's are not plugged into the same power supply. If you are using the
supplied 12v supplies, plug them into different outlets/strips. To be on the safe side, keep the
radio RRC off of the same outlet/strip from the FT-2000.
Maybe that will solve your problem. If not, I suggest you repost your question in the right area.
73,
Mitch DJ0QN / K7DX