So the question is, when applying your coats, how long did you wait between coats? I think that some of us are hinting that if you put too many coats on in too short of a period, you might be seeing a variance in the curing in the parts of the boat that were covered by the rope because those parts were not exposed to oxygen. Try leaving the boat exposed for a few days and see if the marking goes away.

When I'm finishing, I do no more than one coat per day of varnish. For my initial finishing of a boat, I put on six or seven coats of varnish. It is a lot, but the finished results are amazing. Three coats really is the bare minimum for your initial finish. Trust me, wet sand between coats and build up a few more and the results will be even more impressive. After five or six, the finish is mirror like and it can be hard to see where the wet material is going down.

Try a wet sand with a 300-400 grit sand paper and see if the marks will come out. You do it as a wet sand as this will keep your paper from filling up to quickly and will help to minimize burs digging into your finish too much. This grit won't hurt your finish so long as your rinse well between coats.