Good sleuthing. This could explain your issue - with the battery fuse blown, all the charge current was flowing through the load terminals - which means it was likely not being sensed by the MPPT controller correctly, which could certainly cause issues. Before the fuse blew, you had a path through the load terminals from the main 12V bus back to the battery. If you charge from either the truck or the on board converter, this could lead to reverse current to the battery though the load terminals, which definitely has the potential to cause damage.
The easy way to fix this would be to disconnect the load terminals from the controller. If you want to still use the load terminals, you need to find the other path by which the fuse block is getting power and disconnect that, so the fuse block is only powered through the load terminals. You also want to make sure that any other charge sources (truck alternator, converter) are connected directly to the battery and not the fuse block.
Note you can only draw 15A or whatever you controller is rated for from the load terminals. If you have higher current loads (eg and inverter) this won't work.