Did this just start happening? It sounds like you may have deleted/added/changed one or more entries after they had been reconciled. So QBs is showing the $3K difference.
If you think/know this is what happened and you know which transaction(s) was changed, then there may be a quick fix. An example would be if you deleted an item in September that had been reconciled, you realized what you did, added the transaction back in and checked it off as Reconciled. QBs knows the original was deleted and now there is this new transaction that QBs did not Reconcile, but it is showing that it is.
Option 1: If you do know which transactions, go UN-reconcile them. Then take the last statement that you have already reconciled and do Reconcile again. **Not the one with the Opening Balance $3K issue the one before that.** Use the same Closing Date and the same Closing Balance. Hopefully the now un-reconciled items match the $3K you were off before. When you let QBs reconcile these items all should be back in sync. Then take the lastthe missing items from that period will show up and you can mark them off.
Option 2: Unreconcile the last couple of months to where you know everything was in sync. Best/easiest way to do this is with an Accountant copy if you happen to have one or can call whomever does your taxes for a quick favor. They can log in and unreconcile the month in one action.
The other way is to manually go in and UN-check all the transactions and then re-reconcile. It gets real tricky figuring out what cleared in what month. So hopefully you do know which items were changed and the top option will work for you.
