I've never used that particular PIC but based on experience with lots of other types, I suggest you look at the code for initializing PORTB, in particular, ensure no other internal peripherals are using the pins. It's easy to overlook that (example) you might be outputting PWM on a pin then reading it straight back in as though it was a dedicated input. In theory, if the port is configured properly as an input, the pins should float so your pull-up or pull-down resistors should tie the inputs to a fixed logic level, nothing inside the IC should be able to change that. Can you post your initializing code?
Brian.