This all sounds hideously familiar. The first I had a frame resprayed, I put in the stand clamped by the seat tube. That did small bit of damage to a decal. Not a big deal in the overall scheme of things (you have to look pretty closely to see it), but I was not a happy camper. I mean, I hadn't even gotten the bike built up and on the road before it had been schmutzed up.
Since then, I clamp the seat post each and every time. I have yet to mess up a decal that way.