Check out the mastercraft teamtalk forum. People with 06 and 07 boats are having these problems. Some people thought it was the factory cover, (is your new cover a factory replacement?), others think maybe the backing on the vinyl is seeping through. Either way its a problem. Supposedly letting it sit in the sun will really help out, then scrubbing it with a vinyl cleaner. Teamtalk has a huge thread on this, www.mastercraft.com/teamtalk
. Hope this helps.