Adjusting the pull/reach of STI levers with top-brakes (Tricross)
The inline brakes are called interrupter brakes, or cross brakes.

It almost sounds like the pull of your inline cross breaks is meant for V-brakes, while your STI's are set for cantilever. From the details you provided, its hard to say what is going on.

If your brakes are set really loose, then both levers would bottom out before engaging, or would be rubbing the rims.

If they worked before, the shop did some work, and now they don't, well then its pretty obvious you need to return to the shop and have them fix it properly.