Will Hydra Tuner work with transmission shift kit?

[Chris77]

i received my hydra chip this Friday and discovered that there are tunes for modified valve bodies. I installed the chip methodically per the video instruction on hydra help and the chip is working great. Ive only been running the 40 horse DD tune so far because I have an old tired transmission but WOW!! Ive owned my truck for 15 years now and this is the first time its ever been chipped and the first time I ever saw any black smoke come out of the tail pipe. Im impressed! I did notice one thing though...when I press the up or down button on the hydra selector switch it takes a few clicks of the button before it responds. Is this normal.