Welcome to the wonderful world of X-Files pinball ownership! X-Files was my first pinball purchase as well, and though I've since added others. X-Files continues to be fun to play. I don't know that I can add anything that hasn't been said for your particular issue at the moment. If you don't have a manual, I suggest trying to pick one up on ebay. They are great for trouble shooting and looking at specific parts.
Welcome also to Pinside! It's a great community here.
Perhaps most importantly, when you solve it, please post back and let us know what fixed it, so if we run into the same issue, we'll know what to do.
Glenn