So I started a new game on a new clean install. I chose the Hoy as my starter ship and me being me, immediately reshaped the sails. 
With the stay sails I swapped the locator 1 and 2 locations. Then I noticed that they were no longer moving in the breeze, but they did raise and lower normally. I put them back and they work normally.
I then played the beta 4.1 game and used the Castel Freiderichsburg, which has the same sail layout, and its stay sails do not move either.
Both installs are on the same base stock game. Could someone else sail the Castel F and confirm/deny this is happening?

With the stay sails I swapped the locator 1 and 2 locations. Then I noticed that they were no longer moving in the breeze, but they did raise and lower normally. I put them back and they work normally.
I then played the beta 4.1 game and used the Castel Freiderichsburg, which has the same sail layout, and its stay sails do not move either.
Both installs are on the same base stock game. Could someone else sail the Castel F and confirm/deny this is happening?