I have the same problem also, and there isn't any real fix for it, but if you minimize the game and bring it back up (with alt-tab) then it sometimes brings it away. Unfortunatly there isn't much to fix it... I think it is a graphic card unsupported because I never had this problem until my graphic card that WAS supported (an ATI X1600pro) got fried when installing new hardware. I put in an old graphics card that isn't even supported by RaF and I have that bug all the time. The best solution for the settings problem is to just know what your settings will start out as, and you can change them to how you want (so if "High Resource" is selected when you play the game, click there and it will switch to low resource, even if you can't see it).
"It seems to me the humour of Sails is so dry you could strike a match on it and it would be the humour that caught fire." - Friend of Old