A journal entry will show up in the bank reconciliation wizard only if it meets the following conditions:

1. As a blue line.…

If one of the items in the entry is for an account which is the default debit or credit account of the bank journal

AND if the journal entry is linked to a payment

This condition indicates a payment. This payment can be matched with an invoice or not.

OR

2. As a black line.…

If one of the items in the entry is for an account with reconciliation allowed (AP/AR/Liquidity Transfer)

AND if that item is not reconciled (matched) with another journal entry.

This condition usually indicates an open invoice. Reconciling a black line will create a payment and match it with the invoice, thereby marking the invoice as paid.