Ah, PK does have it's occasional problems, though luckily it's not as bad as some more famous coasters. The sensors seem to be a big issue for the ride - I've had to walk away from it on several occasions simply because it started misting and the sensors got wet. They're laser senors apparently, and if any sort of precipitation hits them, they read positive or something; so after each rain they actually have to walk the track and wipe off each sensor until it's clear enough to function properly - that's why it takes so long to re-open after a rain.
The waterboggin only uses one lift, so there must have been something wrong with the particular slide - maybe a branch fell in or something.
AP stops logs on the lift on purpose. If you notice, the lift is set up in several sections which operate independently so that one can stop while another runs. This way they can stack logs on the lift rather than have them going off the drop uncontrollably. There's usually an enthusiastic controller sitting on the booth who slaps hands with everybody - he controls the starting and stopping that you see.