[brianogilvie]

The badge on the OmniFocus icon signifies the number of overdue, due soon, or inbox items in OmniFocus:

If the number is red, it's a count of overdue items (actions and projects).
If it's yellow, it's a count of items that are due soon.
If it's gray, it's a count of items in your inbox.

OmniFocus follows that hierarchy: if there are any overdue items, it will show them. If there's nothing overdue, but things due soon, it will show them. If nothing is overdue or due soon, then it will show inbox items.

You can turn off this behavior in Data Preferences.