First of all, I made a device reset and did a clean install of mach3 (also deleted PoKeysMachConfig.xml in ApplicationData folder). I have my limit switches + probe on pins 34-40. I was following pokeys mach3 setup document and after I set pulse engine to External 4ch without IO and restarted mach, pins 36,37,38 got set as outputs. 34,35,39 and 40 stay as inputs. If I close mach and open pokeys app and set pins 36,37,38 to inputs and then start mach then they again are set as outputs. I even tried to actually configure limit switches on pulse engine tab in mach but those 3 pins stay as outputs.
Before reinstall I had it working but was experiencing the same thing. Every time I started Mach I had to go to pokeys config and click OK, after that limit switches were working fine until I restarted Mach and found those 3 pins to be outputs again. Are those pins somehow reserved when External 4ch without IO (PoExtBusOC16CNC) is used? Using Pokeys57E.

Open PoKeys application, go to Peripherals > PoExtBus and uncheck the 'PoExtBus on pins' option. By default, this should have been disabled.

That option is "PoExtBus on pin 35,36,37". I have problems with pins 36,37,38.
But anyway. that option was unchecked in my case. So I also unchecked "Use PoExtBus", set pins 36,37,38 to inverted inputs (that's what I use for limit switched), sent it to device and closed PoKeys App. Then I started Mach and after it got loaded, I again started PoKeys App. "Use PoExtBus" was selected again (PoExtBus on Pins 35,36,37 was unchecked) and pins 36,37,38 were again set as non-inverted outputs. If 36,37,38 can't be stopped to be set as outputs on Mach start then I'll have to use different pins. Although I would really like to know why it's being set as outputs.

Which firmware version are you using?

4.1.64

Apparently, Mach3 plugin is initializing those pins to support the IO functionality of the PoExtBusOC16CNC, although it is not there. We'll work on finding the issue and fixing it in one of the next releases.

Thanks for looking into it.