Since it's not in the I/O Configuration, that points more solidly to the issue being the module itself. The only reason the PLC would even care that it's in the rack is if it was using it to communicate with something else (IO or another processor),and it would need to be in the I/O Configuration for that to be happening. Since it's not in the configuration, the PLC won't care.
I guess it's possible the PLC could be using it with a MSG instruction with the path manually set. You can verify that by going to the tag window and sorting by datatype. Look for a "MESSAGE" tag and cross reference it. Look at the Path in the MSG instruction to see if it's going out through the module. I would be really surprised to find that the PLC is using the module without it being in the I/O Configuration.
If you want to add it to the I/O Configuration as a test, you can. Just set the electronic keying to compatible keying and the newer module won't be an issue. I really think you're going to find that the module itself is bad, though.