Most likely the PU selector switch is bad. My JTV-89F had only 3 models on a 5 model selector, 1 and 3 were the same, and 4 and 5 were the same models. I replaced the selector switch I ordered from Full Compass, and it solved the problem. It was that way new, but I never listened close enough to notice that there were not 5 different sounds for one setting choice, only 3. I soldered in the part myself and it has been working fine since then. The only way I knew was by connecting it to theWorkbench HD and saw the selector switch showed in it only a switch of models on 1,3 and 5.
Often people think that switches need the contacts cleaned inside with some cleaner, but more often than not, the contacts need some lubrication so they slide across one another smoothly which helps make good contact. Cleaning just makes it worse IMO.