You know I've got the same issue
I normally use WinRAR (not sure why we all don't)
But I decided to download all the free ones, a month ago, to test for the best one to quote (I was updating Memtest Tutorial at the time)
And since then all my Zip downloads when extracted just extract to a filename without an extension
I have since learnt that if I add zip extension, and then unzip the file again, it works.
So then I un-installed all the zip programs and checked the Windows "filetypes" extensions, back to defaults, then re-installed WinRAR, and it's still the same

I even re-checked the "filetypes" again, and confirmed WinRAR is correct
Then I did all the scans (Virus/Malware/Registry you name it) and it's still the same :suspiciou
So I thought, geez I can't even work it out ! Forget it, I'll just add "zip" to the extracted Zip file and just unzip it again.
And that's what I've been doing since !
I didn't try Repairing Windows, as everything else is perfect, just this zip issue (probably caused by having multiple zip programs installed, at the time).
I've learnt to live with it.
