Service Mgr. said he was able to pair the new TPS sensor to the ECM, so the battery in the sensor must be good.
Not really true. When registering a TPMS module you need only the ID that is printed on the label of the module. The TPMS module will not be active until the bike is under way. The registration is a "static" process unlike the KiPass or Key Immobilizer registration which is "dynamic".
So it's quite possible that:
1) The sensor is defective and is not communicating with the KiPass ECU. Perhaps it has a dead battery after sitting on their shelf too long or just failed on its own. Like any electronic device, it's possible for it to fail at any time.
2) The dealer is using the WRONG ID. The KDS3 doesn't really care what ID you put in, it just takes your word that it's the correct ID. If you enter the wrong ID the only way to know is that the TPMS module will never communicate with the bike and you will never see a pressure from that tire. (Sound familiar? I think this is the problem as human error is far more likely than a module failure.)
3) Somehow the dealer got a non-USA TPMS module. The USA version runs at 315 MHz while other versions are 400 MHz or so. Bottom line is that they use a different frequency for communication and if it's the wrong one the KiPass ECU will never "hear" it. The frequency should be printed on the label but even that might be wrong. When I work on these to replace batteries I check them with a scanner radio that can tune to 315 MHz. You can hear them "chirping" when you connect the battery and for a few minutes after. I've not heard of this happening but I'm sure it's possible.
4) There is an issue with the KiPass ECU where it's not registering data from the 2nd TPMS module. Easy test here. Have the dealer SWAP the IDs in the KDS3 system between the front and rear and see if the problem with no pressure moves. If it does then it must be #1 or #2. If it does not, then I'd suspect a defect in the KiPass ECU. Unlikely, but within the realm of possibility.
I find it quite difficult to believe that the dealer is registering the new TPMS module to the bike but is NOT testing it out before handing the bike back to you. But I suppose that's one way to cut corners. I say keep after them. I know it's a PITA to keep having to go back but I'd insist that they test the TPMS modules on the bike before pronouncing that the thing is fixed.