Join Date: Aug 2006
Location: Central Coast, CA
Bikes: Surly LHT, Specialized Rockhopper, Nashbar Touring (old), Specialized Stumpjumper (older), Nishiki Tourer (model unknown)
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I don't know if I understand, but here's 2 cents worth. It doesn't seem to matter which side of the downtube you run your cables on. I bought a used frame and discovered that the cables crossed under the downtube between the top cable stops and the thingies under the bottom bracket that route them to the derailleurs. I wondered if I should fix this "mistake" and did some asking. I found out it doesn't really matter. I recall discovering that Sheldon (RIP) actually preferred routing his cables that way. I built another bike from a frame this fall and crossed the cables from the getgo.
So, I'm not sure I understand the problem you described, but if it helps to know that the side of the downtube you run cables doesn't matter, well there you go.