Most games have legalese in their EULA's against modifying the client software and occasionally take action against players who they may believe have done it. Many games also have incompetent GM and other staff that can get a little ban happy at times.

They could be checking for modifications any number of ways. Theoretically issues such as regular file system corruption, corruption on the wire, malware, etc could make such checks fail and be logged in some way (developers are lazy and like to do a simple md5 check on the files for version control). I don't know of many games that actually send that kind of data back to the server...but who knows.

It could be someone else was impersonating you/your son or accessed one of your accounts via a modified client and was screwing around. It could be that you or your son might have mentioned some minor change to the client on a message board and they are trying to nail you for that (even changing art or text files can be interpreted as a client modification). Maybe they just don't like you...