The two analog extensions go into a fax server, and that has been working fine so I never bothered to investigate that any farther.
I tried a couple other extensions, and none of them seemed to exhibit the same behavior, just this one set, but it only seemed to occur during internal dial tone or when pressing DTMF keys, audio in call was completely normal.
I am pretty sure Tech Electronics is correct and these specific sounds are just comfort tones generated by the phone itself to the user, so it could be a oddity from the recent upgrade, or an indication a set is starting to fail perhaps.
For now I just factory defaulted the phone, and offered to replace it with a refurbished unit, but the customer is going to try it for a while and see if it gets worse (affects calls) or not.
I will update this thread if something changes. I was mostly just curious if someone else upgraded and had these kind of odd, non-service effective issues at all or it was just me... this is only the second site I had upgraded to 6.0PR5 and I have 4 more scheduled over the next week or two on our maintenance customers.