You need to remove the fork legs to install/remove the fork gaiters. They actually usually a good job of keeping dirt and water out away from the fork seal, that's their purpose. If you are getting some leakage just slip the gaiter up so you can clean the fork tube and seal. When you put the gaiter back into place, use some good quality zip ties or bailing wiring to create a tight seal of the rubber at the top and bottom of the gaiter. This should eliminate any leaks you are having. But you are right, having water leaking in like that can definitely cause the problems you suggested.
Scottie