I have mildly moiified my STI the changes are 3 inch exhaust highflowcat turbo boost controler and a utech programible engienmaping sysyem. My problem is the check engine light ,cruse control lights blink and the cruse does not work. When you clear the ECU every thing works but this only lasts a few hours or less

More then likely the utek is causing the problems. You need to figure out what the codes are. I'd probably go back to whoever tuned the utek, unless you did it yourself.