I wish i knew the answer. I don't make cupcakes often but the last time i did i wanted to make a cupcake bouquet with them and had the same problem you describe. i baked them the day before and lightly covered them once cooled with a few paper towels. The next day it was like the liners were soooo moist, and they were pulling away from the cupcake, and toothpick i was trying to insert into them..I thought condensation may have been the problem but the cupcakes were fully cooled when i covered them, and even then the paper towel i placed ontop was only on them loosly, so lots of room for them to breathe. I'm curious to know the answer to this too.
I believe it has to do with the humidity within the enclosed container. When I make cupcakes for my kids and store them in an open container in the microwave or in one of my home ovens, they don't separate and stay moist for days. When I let them cool completely and then store them in a plastic container, the liners peel away. It doesn't seem as noticeable when they are stored in a bakery box. Moisture is the culprit, but I don't have a solution for keeping them moist and dry in a plastic or glass container.
I found that if I take them out of the pan too early the liners peel. Try keeping them in the pan until they are completly cooled and them put them on a wire rack to dry. Putting them away too soon will cause this to happen. Hope this helps 
Out of curiosity, are these standard grocery store wrappers or the pretty ones that are thicker?
I was having the same problem but it was happening out of a container. I've heard theories about it being the recipe, butter versus oil. I was using an all butter recipe.
Here is the kicker: Only about half came off and I was using the same recipe, same techniques, baked on the same day, etc.
I bought my cupcake liners from GSF. They are thicker than grocery store (Reynolds brand?).
I have never had this happen, normally if I have a problem, it is the opposite. The wrappers tear half the cupcake away they are cooked on there so well! I have only used cake mixes, and muffin mixes. Now I have a small cupcake tower to go with my wedding cake this week, so I'm sure it will happen now that I have read about it!
What about checking with a state university-their food science dept, or extension office?? Or if you use a mix, call the 800# on the box.
This was also driving me nuts and it only seems to happen with my recipes that call for lots of good old fashioned butter.
The cake taste fantastic, but peel completely away from the liners (no matter how long I give them to cool).
Swapped the real butter (which is usually my preference) for vegetable oil, and it hasn't happenned since.
The recipes that require real butter I find make a better, denser cake, while the ones that use oil, make a better cupcake (esthetically speaking).
But maybe that's just my experience?!
You know, I made cupcakes last week and never had this experience, but was concerned! I noticed that my cupcakes that rose past the edge of the paper stuck better. I also noticed that if I held it too hard when decorating that the paper kind of popped off at the top, and once it did that, it wanted to separate more. Plus it was grease proof liners, my "extras" were baked using grocery store liners and they stuck like glue.
Maybe fill them a tiny bit more, don't squeeze too hard, and use oil rather than butter if you are using grease-proof liners?
I had never had this happen until recently. It has only ever happened with the scratch wasc recipe from here on cc. I have to say, it's a fantastic cake but it shrinks like you wouldn't believe and I think that was the problem with the cupcakes I made, they just shrunk away from the paper liners. I didn't box them until they were completely cool but the following day at least half of them had pulled away from the liner.
Every other cupcake I have ever made has been with butter. Some rise over the top, others don't. It has never happened before. But with the wasc, I really think it's just a shrinkage issue. The 8" square cakes I made yesterday came out of the oven looking fine then as they cooled they shrunk to about 7".
Something else to think about
AAAAAHHHHHHHHHHHHHHHHHH!!!!!!! It's hopeless! 
I did a test with cupcakes because I never use to have this problem until after I started reading threads about people having this issue.
I baked 2 pans of cupcakes, same exact brand/size pans, same cake recipe, same liners. 1 batch peeled (all but 2 liners were almost completely off) and the other batch 0 cupcake liners came away from the cupcakes. The difference?? 1 batch was allowed to cool for 5 min. and then removed from the pan to a rack, the other batch was left in the pan and the whole pan was put on a rack. The ones left in the pan did NOT peeel.
then it dawned on me why I didn't have this problem before. BEFORE I only ever baked 24 cupcakes for any particular order, and I have 2 muffin pans that each hold 12 cupcakes. I baked them all at once, pulled them out to the top of the stove and was TOO LAZY to take them out of the pan, so there they sat...everytime!!! It wasn't until I had a bigger order that I had to remove them from the pan (so I could use it again) and make more!
Oh wow, I was thinking leaving them in the pan was the culprit!
I had this happen to me is fall. I baked 200 cuppies for a wedding. took them out of the pans after 4 min. put them on racks for another 24 min (while another batch was baking) then I put them in the boxes, iced as I went. All was good, went to bed and the next morning (day of wedding) went to take a look at things and all the wrappers had came away from the cuppies. I used white gp liners. This is the first time I used the white ones. I have used the gp purple liners and black liners for wedding previous to this and they worked great (same process, same recipe). I figured it was the liner. I wrote the company they never responded to me. I recently baked some with the scratch wasc recipe and the same thing happened. i really think it is the liners in my case. maybe i got a bad batch? that is why i emailed the company and was so dissapointed they never responded now i feel like i can not order from them again!
What does "gp" stand for? Is that the brand name?
Wow this is confusing. I find that they don't peel when I remove them from the pan right away, I thought maybe the moisture from sitting in the pan was the culprit.
The only times I ever have this problem is if there is high humidity that day and I store them in a plastic container with the lid on -or- I use the foil cupcake liners. Foil liners hate me for some reason. I never have good luck with them. 
I usually wait until the icing crusts up then store cupcakes in a deep dish casserole pan or my cupcake carries with saran wrap loosely over them. They stay moist and it doesn't mess up the tops. I only put the plastic lid on my carriers when it's time to transport them.
I haven't noticed the length of time they are in the pan making a significant difference. I usually take mine out of the pan after a couple of minutes after coming out of the oven and putting them on a cookie rack to cool.
This is a good question BTW!
MichelleM77 - gp means grease proof.
I finally called the company where I bought them and apparently I purchased silicone coated grease proof liners made for really sicky batters. They were nice enough to replace mine for just grease proof liners.
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