Are you able to install chromium-web-store by dragging and dropping the CRX onto your browser or are you forced to use the Load unpacked workaround?

I ask because the hack I use to install non-CWS extensions from the popup is to download the file and then open it in the browser using a file:/// URL, which mimics the drag-and-drop operation. Chrome's default behavior is to fail and delete any non webstore CRX that you attempt to install in this way, similar to what you are experiencing. If you have not set the #extension-mime-request-handling flag, then changing it should fix this issue, otherwise you may be missing a patch in your build which makes this hack possible.

I had not set that flag. Can't really check now as I've already updated but what you described seemed to be the problem.