For what you spent on on reflashing the PCM (most likely what the dealer did if it was a "software issue"), you could have gotten a Jet or SCT chip and it would have likely fixed the problem. An SCT Xcal 2 or 3 will change shift points,
FYI -
http://www.sctflash.com/DCXC2.php - one of the absolute best things you can do for a vehicle. A noticeable HP/torque gain and improved mileage. Have an Xcal 3 on my 94 Tbird w/32 valve 4.6 and a 9 psi kenne bell blower and it's awesome.
Mine apparently had that problem (I just bought it a week or so ago) and the PCM was reflashed on 2/5. No real other reason to reflash the computer.