Did some playing around just now and the key thing I was missing is the throttle twist grip. I do not know why but DCS does not recognize engines off unless the throttle is fully off.
To to answer my own question for anyone else curious, if you're landing at a Farp or airbase to repair I find the easiest way to accomplish it in the Hind now is to pull both the fuel shutoff levers, rotor brake on, throttle twist grip off. Leave APU off until time to restart after repairs.
Thanks to others who answered as well!
Update - after running repairs and trying anything else I could think of ultimately I went with a clean reinstall and my performance is back to normal. No idea what the issue was but glad it seems to be resolved.
Kevin509's post in Ground crew repair - what has to be turned off?? was marked as the answer