Manual calls out some multiplexers used to read dips (makes sense since you don't want to dedicate 32 i/o lines to it for something that's read once) - so they'd likely be bad, or the pullups on them are bad (low voltage maybe?)

It could also be all 4 dip banks, dip switches of that era aren't great and they are 40+ years old. Some people have used contact cleaner in them, but if you can solder just replace all 4 banks. You can put sockets in and put dips in sockets but that's overkill.

I was out of dips once and I put sockets in and used jumpers in place of the dips.... I wonder what happened to that board? probably in one of my machines I never open.

To do it right you have to disassemble the switch (the contacts are all inside, little bits of metal). Might be best to have a pro look at it, there's no replacement atari boards so you don't want to mess them up. Some dips aren't able to be disassembled at all or you have to remove them anyway, so you might as well just replace.