Shifting Flare

[woerthinny]

Hello,
I purchased a Heavily Modified Phoenix Chip for my E99 F350 this July and within the last month noticed that the tachometer jumps 200-300 RPMs as the truck shifts into overddrive. Today I took the truck to the shop that rebuilt and installed my transmission in January 2011, and they called the problem a shifting or transmission flare. The flare happens in the 65 and 80 hp daily driver tunes as well as the 100 hp race tune. It did not occur in the modified stock tune. I haven't assessed it in the tow tunes as I don't use them very much. They said that the flare is not a problem yet, but it will become one over time, and suggested that I contact you folks to see if it is a potential tuning issue. I know the transmission has a Billet torque converter, a shift kit, and an upgraded valve body. I haven't been able to find my paperwork, but the shop has a record of what products they installed, and are willing to discuss specifics with you folks if that would be helpful.
Let me know what you think is the best way forward.
Thanks,
Brandon