Honestly, the way you describe it seems pretty straightforward and confusing to imagine what could be wrong. I can only think up two possibilities:
1) You checked continuity within each individual segment (switch to ConnectorA-Male | Connector A Female to Connector B Male | Conn B Fem onward so on) and those were OK. However it could be the M-F connection within the joined connectors is not good. Join paired segments together and run your continuity check again.
2) A conductor/wire is frayed and there is a momentary short/break when it curves and flexes into a certain position, or it is getting pinched, such as when you close the coin door, or set the pf down, or something. Much more bothersome to locate. Connect your meter on continuity check and move things around to see if it quits.