Although I've not experienced the problem (I have several Gensets, both MTH and Lionel), it seems to me that the easiest solution in some/many situations, and especially with FasTrack, would be to add one of the short FasTrack fitter sections (they come in various lengths) between the switches to separate them a bit.
I don't have any switches that are directly connected to a second (or more) switch, but on my FasTrack layout the Gensets perform just fine through the various switches I do have.