> It's not configuration bits either. 

Hi Jared,

it'll be analogue. eg, for an 18F452 you need to add

movlw   0x07     ;all digital
movwf   adcon1

for an 18F4550

movlw   0x0f     ;all digital
movwf   adcon1

Check the A2D section in the manual for your specific PIC. You
may need to set other registers like CMCON, ADCON0 etc. I'm
guessing the pins you're having trouble with will be analogue i/p

> movff PORTx, PORTB

That immediately jumps out at me as a potential cause for read-
modify-write problems when x=B. Particularly at high speed and/
or with some loads. Not saying you will have a problem, it just
looks iffy. Also, PORT is generally used for inputs, LAT for
outputs. Two separate I/O registers was a major port improvement
introduced with the 18F series

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