I followed your general work-flow and had no issue:
1. Opened an image file
2. Dragged out a rectangular shape using the rectangular Marquee tool.
3. Edit menu>Stroke(outline) selection - width=3px, placed stroke inside
4. Used paintbucked tool with contrasting foreground color to fill the active selection
5. Also tried Edit menu>Fill selection ----no problem.
Try placing the stroke inside.
If it still does not work for you, reset preferences to default. To do that, go to Edit menu>General and reset on next launch.
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