Thanks to everyone who replied to my inquiry! We had just installed our QA machine and shared the transport directory. I was attempting to test the tp function with a tp connect, which started this whole process.
After some research, I found that as of release 4.5, one is not supposed to edit the TPPARAM file directly, but through STMS. Neither do you have to run SE06 after a standard installation, since STMS is smart enough to initialize the CTO if it has not been done previously.
Therefore, we have decided to upgrade our kernel, r3trans, tp and import/adjust our instance profile, (which require a trans dir path), before returning and setting EVERYTHING up through STMS.