I doubt Pete is tossing his camera and lens into a carry-all bag without a lens cap.
You might be on to something and potentially it's the lens cap itself that's doing the scratching? Like Fish, I'm a fan of the Hoya HD2 protectors and have either that or an older Tiffen UV filter on each of my lenses for protection. I've been curious as to whether my lens caps are scratching the filters, but haven't seen evidence of that yet. It could be that the filters are taking the brunt of the lens cap edges and doing a better job of resisting scratches.
Either way, it does sound curious and I hope you're able to figure out what's going on.
Since none of my other lenses have any scratches, this is what I'm thinking. The 18-140 front element sits almost flush so when I put the lens cap on I have to make sure that I'm holding the cap really horizontal other wise it will touch the lens. (If that makes sense. ) All my other lenses are more recessed. Even my Tokina that has somewhat of a bulge sits more recessed. I think I'm just going to buy a filter and use that as a lens cap.