Ok. well, I'm still confused. First of all, the HM will (should) function on its own without a rPi when plugged into the 12V power supply. (unless you have an older HM?) So if the HM's are working you should see NO PIT PROBE on the display when plugged in (without the rPi)
The way the power goes on the HMv4.2.4 is:
12VDC in from PS
OKI board converts 12V to 5V
MCP1700-33 3.3v Reg converts 5v to 3.3v
OLDER HM's were a bit different, 12v in, OKI to 5V, then 5v out to the rPi, and the rPi would return 3.3v to the HM. There was an OPTIONAL 3.3v regulator on those boards that would allow them to work without the rPi.
In either case, it's 5VDC from the OKI that is getting fed to the rPi...
Pins 24 and 26 on the rPi header get +5VDC from the OKI
Pins 3,5,6,7 are used for communication to the ATMega
and there are a whole bunch of grounds on the rpi header
On older HM's there would be at least 1 pin with 3.3VDC coming back from the rPi
So you should check those voltages and also report what version of the HM board you are using?
Always helpful to plug the rPi into a HDMI input of a tv or monitor to see what is really going on as well..