what's your rev limiter set to?
what's your max shift rpm set to?
what's your shift speed vs gear tables set to?

These are just a few questions that I ask when trying to troubleshoot issues like this. Shifting requires the speed (mph) requirement to be met first (along with fluid pressure and other things), then the PCM will allow a shift at the desired WOT shift RPM value. Otherwise, if you hit 5500 (if that's your max RPM), the vehicle will bounce limit until that speed requirement is met (in whatever gear you're in). Sounds like your tuner has a little bit of homework to do.

Good luck!