The In Progress gadget should show any issues that are the In Progress status so it's a bit odd that is only showing the Epics. One thing I would verify is whether or not the the missing items are assigned to you.
I tested this with an Epic and three stories in the Epic. The Epic and the first two Stories were assigned to me but the third was not. When I viewed the board that issue did not show up but when I went back and assigned the issue to myself it showed up along with the other two Stories and the Epic.
Hopefully that provides some insight.
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