The first several batches in my 15-gallon BoilerMaker mash tun were also fubar. Recirculation would start out fine, but eventually it would slow down, then the pump would start to pulse, and flow would eventually stop altogether. If I was there to catch it, I could start it up again by opening the valve on the output of the pump, but it would just do it again. I recirculate on a Blichmann burner, as low as I can get it without blowing out, and my un-scientific recollection is that it typically occurred while the heat was on trying to maintain or raise the mash temp.
I surmise that the issue at least in part, was caused by a flow rate that was too slow, and wort underneath the false bottom that was starting to boil. Bubbles from the boil would get trapped in the pump and cause it to seize. Of course, I can't see what's going on underneath the false bottom, but that's my theory and I'm sticking to it
Opening up the flow has solved the problem for the last five or six batches. (I also replaced the impeller on my March 809 pump with the higher-flow impeller.) More flow, less concentration of heat under the false bottom, no bubbles. That false bottom can handle a substantial flow rate without clogging.