Possible power top issue.
 

Hey guys, I noticed this morning when closing the top on the Box that the passenger side of the top seems to be slightly lagging behind. The top still closes fine but the passenger side is just a little behind the drivers side. Is there an adjustment or something I can do to remedy this problem???

Check the push rods and motor under the clamshell and make sure you haven't broken one of the plastic cups on the push rod. It's fairly easy to see the parts with the top in service position. See 101 projects Top Repair pages:

Pelican Technical Article: Boxster Convertible Top Repair - 986 / 987