I have had several issues with my Intellicenter/Intelliflo comms.
First issues was that the comm port on the main PCB stopped "working". This happened to me concurrent with switching out of Service Mode right after I had upgraded to the ill-fated 2.006 (?) Intellicenter firmware. Going back to the older version of the firmware didn't help. However, I moved the comm connector for the pump off the main board and attached to the surge board. This fixed the issue, and comms restored. Another TFP user reported same issue, with same fix.
Shortly thereafter my IC40 died. It was still under warranty so Pentair sent a service company out to replace it. There were friendly and reasonably competent, so I asked them about the Intelliflo comm issue (my Intellicenter is out of warranty). They messed around a bit with no luck restoring the main PCB comm connection. One thing they did was swap the comm wires on my two Intelliflos.
A couple weeks later both pumps stopped responding, completely. A couple weeks later one started showing Display Not Active and intermittently ran schedules. The other still had no comm connection. In order to control the pump manually, I disconnected the comm connection on the Display Not Active pump and left it hanging. A week later I reconnected it and all comms restored. But not the other pump. So I pulled the comm wire from it. I noticed it wasn't "locked" on by twisting - I could pull it straight out. I looked at the connector and saw water inside. I dried it out and, voila, that pump reconnected.
My theory is that the service techs, when they were switching wires, didn't lock the connectors on the pumps. We'd had a fair bit of regular rain so I think the water seeped into the comm connectors and was screwing up the RS485 signal. (The connectors have a o-ring that doesn't compress until the cable is "locked"). Note I have the supposedly bad 3.03 pump firmware but haven't seen any issues previously.