For the liners two things seem to be the biggest culprits, cheap liners...I've only had this happen with the new Michael's celebrate line which I think is crap...design completely faded and the liners came off.
Second, for very moist or high fat content cupcakes sometimes the liners come off. How long do you let your cupcakes cool in the pan? If you let them sit too long then condensation forms and that could effect the liners as well.
As far as baking in advance cupcakes can dry out quick. I did an experiment last week with left over batter. Put the left over batter in cupcake liners in my cupcake pan, froze for a couple of hours, placed in ziploc freezer bags and froze for a week. When I needed them, pooped them into my pan and straight into the over. Worked like a charm. In my mind I felt the cupcakes were a bit more dense but that could be me just over thinking it because I knew I froze them.
Also these are doctored cake mixes, I'm not sure how scratch batter would handle being frozen. I got the idea to freeze the batter here on CC
Hope that helps.