Thank you for this advice.  I didn't do EXACTLY this, but it inspired another idea that got me to discover which transactions are causing this issue.  I found the transactions.  They are all the same in the sense that they:

1. Are checks written to the same vendor.

2. The debit side of the transaction hits the same GL asset account. 

I did the following troubleshooting steps:

1. Thinking the issue might have to do with an improper setting for the Vendor used on the check, I deleted the check entry and I made the same journal entry as a general journal entry and not a check.  This removed the use of a Vendor.  This did not result in any change.  I was still off by the same amounts. 

2. Testing the General Ledger Account used in the check,  I created a new General Ledger account as a subaccount of the old one being used on the checks.  I edited the checks to use this new GL account.  This produced a positive result!   My SoXF balances now roll properly and these problematic entries are now being reflect on both the ending and beginning balances for both period's reports. 

Now -

I have updated these entries and my reports are fine.  However.  I still would like to understand what was wrong with the problematic General Ledger account that was being used.  This is bound to happen again. I am doing a side by side comparison with the old one and new one and the only difference is that the good one is a subaccount of the bad one.  I can't see any setting on the bad one that would tell me why this was not being reflected on the ending balances of the cash flow statements.    Any ideas of what I caa look into?  Thanks.