How do I fix a problem with the beginning balance when reconciling?

If the reconciled opening balance has changed, a reconciled transaction has been added, modified, or deleted.  To determine the source of the change, I suggest you compare the running balance of the account register in the current datafile with the running balance of the account register from a datafile backup saved when the account was last reconciled.  One way to do accomplish this is to print the registers to text files.