The nomenclature in MD is different than in Quicken, but all the same distinctions are there.
In MD, downloaded transactions are marked with a solid blue circle. When the transaction is "Confirmed" (that is, you have decided to accept it into the account register) the solid blue circle becomes a blue outline of a circle. The blue circles have nothing to do with the status of a transaction in terms of reconciliation.
Under the "C" column in the register, the indicators are blank (not reconciled/cleared), an orange/yellow diamond (being reconciled/cleared) and a solid green circle (reconciled or Cleared).
There is a setting of interest here. Under File-->Preferences-->Network there is a setting "Mark Transactions as Cleared when Confirmed". If that is checked, each time a transaction is confirmed (solid blue circle to blue circle outline) it will be marked Cleared (with the solid green circle). Maybe that is how your MD installation is set up?