As you can see from the schematic the probe circuits are quite simple. They used to connect directly to the ATMEGA but a few versions back Bryan added the RC filters, they are made up of the resistor and capacitor that are in the circuit, then there are the pullup resistors, that's it, not much to go wrong.
If you have a lot of flux on the board left over from soldering you might try washing with isopropyl alcohol and a soft brush (let it dry before powering up!)
What type of probes do you have? There were some Maverick probes that have plugs which are too long and you cannot insert all the way in, you have to pull them back out of the jack a little bit to work.
In the HM config each probe has a "Probe Type" setting, which can be set to Disabled, Thermistor (standard probe), Thermocouple, or wireless probe. Set that to Thermistor. There is also a "Probe Coefficients" setting which you need to select to match your probe type.