I've been experiencing the same thing. mine was telling me I was at 1790% of the deployed science from the moon, and I hadn't even deployed there yet. this was in a new game save since my first post.. I've since started a 3rd new game save to see if that changes anything. making lots of quick saves prior to deploying science just to have a place to go back to prior to the science bugging out on me.
in another post someone said that it is required that you have one of the little deployable antenna's to transmit the science if you are not at KSC, but the KerbNet shows my station on the mun is connected, so that doesn't make seem to jive. That said, my new station in my new game save has not transmitted yet, so I may need to send up a antenna once I unlock it..
so the deployed science seems a bit weird or buggy at this point. I would like to see some details out on the Wiki on it from someone who knows the details.
I only run the Alarm Clock MOD, btw.. not sure if that is something that conflicts. wouldn't think so, but you never know.