I recently had some similar problems of uploading zipped file.gdbs to Portal (10.4.1). We finally figured out that moving from Chrome to IE fixed the problem. This was under Win7, IE 11. Https only Portal (I suspect this is key to the issue?)
Chrome is: 54.0.2840.71 m (64-bit)
As I result, I'm staying away from Chrome when doing any admin work in Portal, for now at least.
This was one of the most bizarre and head scratching browser incompatibilities I've ever seen.
Sorry to hear Jake has had issues with IE11 but since Edge solved it, sounds like that means Win10 was involved?
It would be nice to see a gotcha thread started for Portal for these types of issues (and hopefully fixes).
I don't believe GeoNet has the concept of a sticky thread though, does it? Sticky if things keep being added, otherwise a thread falls off the page until touched again?