Actually, I have had this happen to me a couple of times over the years. Both times I was unsucessfully trying to check in online the evening before morning flights and upon arriving at the airport, the ground staff acknowledged that there had been a problem with the online system and checked me in without charging me.
The only thing is that it is difficult to know whether the problem lies with you or with ryanair until you actually get to the airport. Do you have the latest version of adobe reader and the latest versions of your internet browser (firefox, i.e. etc...)?
Maybe try another computer. If you still dont have any joy then its probably safe to say that the problem lies with the airline website. If this is the case they should allow you to check in at the airport without charging you.
Good luck
Anansis