I have an exhaust vent in my basement (Amerivent Type B) which takes the exhaust from my gas furnace and water heater goes out the basement wall, and up my chimney. A little bit water is coming in to my basement from this vent. It looks like this has been happening for quite a while based on drip marks on the floor (since before I moved in in 2007) but it recently lasted long enough to run back along the pipe and into my furnace, shorting it out.
I took off the vent from the furnace and reached in there, there's a little dampness where it turns 90 degrees to go up the chimney but none before that making me think it might be a small leak at the top of the chimney but the amount is small enough that it could condensation (if the water heater exhaust could cause condensation).
Can/Should I fix this or just leave it as the previous homeowners did? How can I prevent it from running back into my furnace again (seemed to go between the inner and outer wall of the vent pipe)?
Edit I shined a flashlight back there and it looks like some leaves had built up.

I took care of them with a shop vac. Will that take care of my problem (until the next time they build up of course)?