If everything was put back as it was (wiring/ground points, etc.) I'd maybe start looking at where some of the ground wires are screwed into the frame to check for overspray. If paint got on those areas (and into the threads), it could be preventing as good a ground for the system as there was before.

When you take it back for the hood respray, ask the guys who worked on it which ground wires in particular they remember having to take off and put back on during tear-down and reassembly for places to start looking.