Here is one problem I have with my track up. It comes when the boat sits on the trailer for a month or so between races, birds sit on the mast and crap in the sail track! And spiders seem to like to build little round fuzzy egg sacks in there too!

I always wash it out thoroughly the day before I go to a race, then spray it with dry lube, which is easier to do with the track up.

I guess that would be one reason you might want to store it the other way round, might stop the bird crap but the spiders might like it even more.