The Check Reconciliation Report will not include any transaction in the Summary section that do not have transaction types and thus will not include the items in the calculation of the Ending Bank Balance. You will see transactions without types listed below in the Cleared Transactions section. The Summary section groups the transaction by type and the Cleared Transaction section just selects by cleared date and will identify the blank transaction type as "Check". You have blank transactions because they were created from a journal entry post.
When you process journal entries to record interest income, bank fees, transfers or other activities that don't typically come from the Gift or AP modules but affect your checking account, you can put Yes in the Create AP field and they will automatically create transactions in Check Reconciliation. However, they will be created with a blank transaction type. You need to change the blank transaction type to a valid value. Make it part of your process to code the transactions that come from GL.
To do this coding, find the transaction in the Transactions tab and click Edit Transaction (upper right hand corner of the screen). Select the appropriate type from the drop-down. This will only affect the category it is placed in. It will not change a value from a positive to a negative or vice versa. The Transaction Listing Report will assign a value of "G" for general when displaying the transactions, but certain ways of running the report will leave these transactions off.