I got a chance to look at my HMv4.0 to investigate what went wrong with adding the RC filters. As I noted earlier, the RC filter resistor must be placed between the ATMega and the pullup resistor, unfortunately not in the convenient position at the end of the CAT5 wire. In order to accomplish this there is no other way than to cut the short trace between the pullup resistor(s) and the ATMega as shown in this picture:
(The probe inputs to the ATMega are the first four pins from the top corner near the probe jacks, Pit Probe being on the corner with food probes counting in from that. I marked cuts for the Pit Probe and first two food probes, leaving the last probe/ambient temp alone)
It's not too tough to cut the trace(s), even after the HM is built up. After you cut the traces those pins on the ATMega should be isolated from the probe jacks, do yourself a favor and check for lack of continuity before you proceed... I made the three horizontal cuts and installed the caps and resistors and thought I was good to go, the two food probes wire perfect but the pit probe was wonky... Took me a minute to realize the pit probe has the trace routed a bit different from the other probes and so you have to cut an additional trace, which is indicated with the vertical line. This trace is between the ATMega and the probe jacks, kinda tight but there's nothing else down there but the ground plane so just get a look at the trace with a magnifier and then cut roughly in that area with a razor blade/knife. Now you need to add a jumper wire from the Pit Probe to the pullup resistor since you had to cut that trace. I chose to jumper from the probe header instead of the pit probe jack because it was closer. Once that trace was cut and jumper installed the all probes were working nicely with RC filters in place. I tested them in hot tap water and compared to my HMv4.2 and readings were spot on.
Here is a picture of the resistors and capacitors installed on the board after I cut those traces.
With all those resistors clustered in there at the ATMega it can get a little messy, a cleaner alternative would be to carefully solder in SMD 100K resistors between the ATMega pins and the pullup resistors. Unfortunately I didn't have any 100K SMD on hand so I soldered in a 10K for the pit probe just as an example.
With the traces cut, resistors installed and caps across the probe jacks as shown the RC filters are in place for both the onboard probe jacks and the CAT5 probe jacks as well.. and are working well...