car only starts and runs with scanner tool hooked up to it

it does turn over tho.......but makes a clicking noise

Sounds like when you down loaded your car data to the reader, they will sometimes retain it. Try going to a page on the tool with key on, engine not running, and download you car's diagnostic and run data back to it's OBB2.

thanks I did what ya said but still a no go

For some reason it is still running off the engine tune and set up rather than the onboard computer. Only a shop with the large computers may be able to get it to convert back over, but they gonna charge. Sorry couldn't help more.