Two (somewhat similar) issues:
1) Flaps automatically raise if you stop taxiing. They should stay down until you manually raise the flaps.
2) Helicopter landing gear still does not have an OPTION to choose between auto-raise/lower gear or MANUAL raise/lower landing gear in the difficulty settings. Trying to hover low above trees is NOT "stealthy" when your landing gear is exposed like a penis hanging out of an open zipper.