Here's a possibility, it may not be malfunctioning but just part of the system that makes difficult. I think the cruise is a little weird depending on when you turn it off. I can't exactly remember how it works, but there are some situations where when you turn it off, it is still somewhat engaged and will still limit your speed. I know if you turn it off going the set speed it won't let you go faster until you slow down. There may also be something where if you turn it off while going slower it's still engaged.

I just always turn it off now when in neutral or with the boat off. Or actually to be honest, right after I forget to turn it off and go to get up the next skier and the boat doesn't go anywhere.... back to neutral, cruise off, ok now we're good.

When this happens to you, when did you toggle the cruise off? Also, going in reverse won't reset anything.