Owl, from your video there's still some things you are doing that I would consider to be 'wrong', though they may not be the cause of your issue (at least, when I do them I still don't get your fault). If the video above was created before my earlier post please disregard the following.
1) You are still creating a final point very close to (or trying to be co-located with) the first point. This is not necessary and will lead to a badly-formed corner as closing the curve does not merge the points. Closing the curve creates a line from the first to last point regardless of their proximity, so best to open the editor after creating the second-last point.
2) You appear to still be accessing the Path Editor by double-clicking one of these almost-in-the-same-place points rather than double-clicking the path. This could be affecting one of the point's properties (such as converting it to a curve).
3) Finally, I would always de-select 'Extendable' when closing a path. While this shouldn't make any difference, in the interests of determining this fault it would be worth taking this step.
Noteworthy in your video is that the second extrusion (at 1:36) works correctly, this suggests your earlier observation "Once it produces extrusions with no caps, it will do it continuously for all further extrusions" is not correct. While I'm no closer to replicating this fault, if you could try the same test as in the video above while observing the steps I've listed it might help us get a bit closer.
