when you say "lose control" do you mean they do not respond in game, or they respond randomally and wildly?
a few things to check:
unlike AH one auto combat trim does not turn off with the input of manual trim from the rotaries. back in AH one you banded the rotaries then mapped an actual key press. in AHII they are an axis.
if you disable auto combat trim in flight preferences it will not come on unless you manually put it on.
if you have it set to on, to get the trims to respond you must turn it off manually by hitting Ctrl-X i believe.
also since these are axis, you must calibrate them just like the rest of your stick and rudder.
lastly, in the JS controls window the wave form graph on the axis inputs does not show range of motion for the rotaries, though they do work in game. maybe it's a bug, maybe it's a feature, i dont know, it doesn't really matter to me.
hope i explained that well enough for you, i use that setup, and manually trim all the time with no problem.