Hey!
I take Yasmin, and while I've not experienced flaky skin myself, I know it's also used as an acne preventer (as well as birth control). As a result a side-effect is probably dry/flaky skin, so maybe it's that. It's weird it's just on your eyelids though.
There should be a small booklet in your pill packets that explain the side-effects and all that jazz, so take a look at that!
Obviously I'm no expert, but assuming the medication is making your skin dry and flaky, my best advice is to start moisturising/moisturise more often. If that doesn't work Google it more thoroughly/go to your doctor for advice.