Sounds weird. When you experience the problem, does the flipper stay up for too long when you half-release the button, or does the flipper stay down when you re-press the button?
In flipper test mode, verify that the power winding and hold winding work for both flippers.
In switch test mode, verify that both switches for the flipper buttons work (upper flippers and lower flippers, even though this game doesn't actually have uppers). Verify that the end of stroke switches work.