If you took the code from the old CP3 and loaded it to the new one then in theory it should work the same.
A couple of things you can check:
* Firmware - see if you can load the same firmware version installed in the old cp3 to the new one. Probably a long shot but there have been issues with some of the later cp3 firmware
* IP Table - I suspect this is more likely a cause for some of your issues, check that both processor IP tables are the same
