Only a few ways water could fill up the pipe - broken or leaking gaskets, broken or leaking water jacket and backflowing of the water into the waterbox and back into the chamber. These 1100s are awesome, but were a dealing with engines and exhausts that are usually 10-18 years old. Ive seen quite a few chambers that have broken jackets. My suggestions, try the hump in the exhaust outlet first, if that doesn't work, then pull the entire exhaust system and pressure test.
SM