Which Sharpie did you use? I've found black and the metallics to be quite color permanent, even when exposed to the elements. We've done some informal color fastness testing on both the gold and black, in which one surface was left exposed to ambient light 24/7 and the other surface was covered with opaque black mat board. I think my Crayola rep dropped off those markers back in September or late August and I've yet to notice any color shift or fade. I'll be very interested to hear which you used.

That said, I've used the metallic Sharpies over freshly painted tubes and found them to be very easy to use and control. My bikes are stored indoors, and if memory serves I've clear coated the lining every time they've been added. The gold lining over black tubing has an elegance that appeals to my own design sense - here's the "crusty mystery frame" I shared with the forum last year, after detailing with a Sharpie: