The trans is still under warranty so go back to your dealer and explain the problem, asking that a tech ride with you so that you can demonstate what's happening. If it can be duplicated, they'd have no logical reason to ignore you or not address your problem as (IF it's a trans problem), they'll be paid by Volvo to replace it again if need be.

There is no need to ever DL software for a new (reman) trans. The SW goes into a trans ECU but that ECU cares less what trans is in that car (original vs reman). The ECUs adaptation should be reset (in theory) but that's about it. The SW PNs should be checked via the dealers Vadis PC to make sure that it has all the latest available SW. For '99 S80s, there are several dealer only tech net notes (available through their VEN network) which give plenty of detailed info about SW and available DLs. I'd assume that they would have done all that BEFORE replacing your trans however.

To date, I have not seen a bad reman S80 trans. Every one that we've installed is still doing OK and we've been replacing them since fall '98 when S80s first came out (not unusual as the first ones had problems).....GM trans!