Whenever I had running light issues on our 2000 Dutchstar pusher, it was usually poor grounding. If your running lights around the top perimeter of the coach are all working, start at the rear tail light fixtures and look at all of the grounds. Or vise-versa, if the perimeter marker lights are not working, start there.
I had one instance that I recall where I had a corroded ground point on the "sleeve" of the bulb (like a regular 1157 brake/tail bulb) in a rear brake/tail combo fixture and it caused all kinds of weird issues............ And of course, check all your fuses too.........
Hope this helps.