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When I first 'discovered' this problem and looked through this thread I checked the Chrome:Plugins and Flash only had two entries (I was checking because someone else had previously suggested disabling the built in Flash, but at the time that's all that was showing for my PC, despite me having the latest Flash installed...).
Anyway, I just checked again today following your post and Lo! there are now three entries. For me, the Pepper version was already disabled, but now I had a chance to disable the built in version and give the external version (the one in the Windows\System32\Macromedia folder) a go. I now appear to be back to proper Flash functionality. I don't yet know whether it's full functionality, only time will tell.
I hope that the attached screenshot will help others to enable/disable the correct combination of Flash.