This is what I've been using for years on door, trunk and sunroof seals. You can get it at ACE or most autoparts stores. You apply it with a lint free microfiber rag rubbing it in. It really helps squeaks that sometimes we think are suspension related - when in fact it's the rubber gaskets that flex with door and truck panels under stress.
As rlouie said above, you could have pollen or debris embedded in the gasket area, or not necessarily the "gasket" but the metal/glass mating surface which you would not notice because it's hidden when the roof is opened.
303 Products Aerospace Protectant
"100% protection of UV caused slow-fade with regular use"
"For inflatable boats, wet/dry suits, tires,door and trunk seals,and under the hood rubber"
303 Products 16Oz Aerospace Protectant (30308) - Protectants - Ace Hardware