Good question! I think it depends on the brand but am not sure. Hopefully some others chime in here too. 
I haven't worked with really nice or expensive liners, that being said i suffer from the same thing. since my liners are cheap what I do is I double them up before baking. When they come out you only see the 2nd liner and it looks way better than just using one.
I have the exact same problem, but even doubling did not help 
Someone at my ICES meeting suggested using a not so expensive liner and after baking put that into your pretty liner. I don't do cupcakes much, but just a suggestion.
I bought some pretty ones at the grocery store that have foil on the inside and pretty paper on the outside. Reynolds brand - pretty black and white scroll pattern. Foolproof - and I should know! They stay beautiful on the outside and the price is reasonable.
I'm not sure price really has anything to do with it. I purchased some very pricey liners because the same thing was happening to me (pretty b4 you bake and blah afterward), but it didn't make a difference. I did notice once that I accidentally doubled wrappers and it came out a lot better. So I'm going to try doing that from now on.
I just had this same problem with cupcakes I made recently. I didn't even post the pictures here on cc because the liners looked so bad after I baked them. I'm glad I ran across this posting. I will bake my next cupcakes in another liner, then add to the prettier ones for a cleaner look. Thanks for the suggestion. I ended up using an empty cupcake liner on the smash cake and the BC center bled thru, yucko!
Thanks
Reynolds foil liners have been 100% perfect, so they became the only ones I use in my business. I have experimented with plenty and these take the worry out of my presentation.
Same here!
The Reynold's liners are called staybrite and they are the only ones I like to use anymore.
The only true thing that works is grease proof liners. They of course are more expensive but worth it. There are many colors and designs out there. I would try Globalsugarart.com otherwise just buy the white ones and make the designs on top of your cupcake. You'll notice you don't see the pros using fancy liners.
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