I've been having the exact same problem. The discrepancy report is counting any transaction that was edited for any reason against the beginning balance. They say the amounts were changed, but when I check them individually, the only change was adding payees. 

Adjusting the opening balance entry isn't an option - that was several years ago.

I can't create an adjustment to zero it out because that's not correct either. Any thoughts?

There should be a way to approve a transaction as it is to take it off the discrepancy report and set the beginning balance back to the correct amount.