The Online Journal Entries Report looks for gifts with the System Defined field of Data Source marked with Online Gift or Online Registration. If either of these are checked, then it makes the gift "online" for the purposes of this report. This field is found under User Defined Fields on the gift record:
eTapestry Journal Entry example

If the Online Journal Entries Report is missing online gifts, review the following:
  1. On the missing gift, make sure "Online Gift" or "Online Registration" is marked that the System Defined Field > Data Source. (Note: These are marked automatically for transactions from eTapestry online DIY forms, eStore (Cart), and Personal Fundraiser. If you enter gifts or re-enter a gift, mark this so the transaction is "online" for the Online Journal Entries Report.)
  2. Review the starting query to ensure the gift appears in the Query Preview.