In the third episdoe the script has C-3P0 telling Artoo that if astromech droids were smart enough to have been given voice boxes then they wouldn't protocol droids as counterparts. When Capt. Antilles asks C-3P0 why he has been paired with an astromech droid C-3P0 tells him that they found little need for protocol droids on this mission.

This was done well before the TPM, and it is insinuated that when C-3P0 was paired with Artoo it was the first time they had met. So, by the time you get to episode III of the radio drama and the first appearance of the droids, they have been working together for only a short time.