The flaps are spring loaded to fold in when you put the top UP, and forced to extend by the cables when you put the top DOWN.
If they aren't folding in, then there is a bind in the flap swivel point or the cable.
The cables are very hard to lubricate, you can try drizzling some lubricant in and let gravity do the trick, or you can completely remove the cables and soak them overnight in lubricant.
Consult your local motorcycle / bicycle shop, they might have some better tips on cable lubrication.

Here's a good solution :
http://www.jpcycles.com/product/9100...FQYoaQodoqEAXg