If your doing it manually and just verifying to the GL Balances....and not using Bank Services in any way, then the only option is that you missed something and need to go over everything again doublechecking your work and you will find your issue. 

Once you have your manual reconciliation done then I would suggest you start using Bank Services to do you bank reconciliations. Much quicker and easier. 

I've checked everything multiple times with the GL Detail Report. What would be the next level of investigating that I can do?

I can't start using Bank Services to fix this issue. I need to find it manually. So I might do that in the future, but to solve this problem, I need to find a way to researching it further on Sage. 

It could be something with how Sage configured a certain invoice or something along those lines. How can I research that?

Well, manually reconciling your bank account should be pretty straightforward. If you want you can use the drilldown to drill down from the GL to the source transaction. Then you can see how it was entered in the source ledger. Not sure how that will help you reconcile. Also check to make sure your beginning balances have not changed. Other than that, I think you might need a second set of eyes to have a look and find the issue with the reconciliation. 

Beginning balances are same. There's been other eyes looking at it too. 

So basically, the only tool Sage offers to verify this info is GL Report? That seems strange. There should be some other way to investigating. 

What other information would you like to see? 

I'd like more detailed information for each day. So example, the GL Detail Report gives a total of each day but I'd like that broken into transaction reports. 

The bottom line is everything on the GL Detail Report matches the A/R deposits from the bank statement and AP check report. Yet it's not balanced. So I need to find out where the problem is.  

The bank is it's own ledger and every once in a while it goes out of balance.  Sometimes you have transactions that have been cleared in a future period so you have to put in a bank entry to balance the bank and not impact the GL.  I know that you want the bank to balance but at some point you should put in a bank entry that affects the bank's GL account. That will keep the GL balance the same but will get your bank rec in balance before the holidays. ;)