No, have'nt replaced headers or pins, will give that a try when I get a spare minute.

The reset doesn't happen when flippers are used, only when certain switches are activated.

Thanks for the tip Nino, I will update here when I have solved it.

Chris,

Couple of things.

Did you remove the middle bracket (which use to sit on the top edge of driver board?

Also on the r/h/s of the rottendog board - from memory it doesn't use the middle screw hole.  The factory bracket is three holes and it may be grounding out part of your switch matrix.  If its there I'd cut the hole off the bracket (if this makes sense)...