It is a bug in the Adaptive MPC block where it checks for the correct dimentions of the input ports. For some reason it does not accept a vector signal, but checks for a matrix signal.
I added Signal Specification blocks to all the "MPC Matrix Signal Check <>" subsystems to explicitly state the dimentions.
I found this subsystem by following the link in the Diagnostics Panel, and disabling the link so that I could edit the block locally (not the library block).
That cleared up the error.