The "Download folder" and Chrome's Download Folder may not be in the same location.
Maybe it's that.
I may have asked this or similar a long time ago. I downloaded a pdf file using Chrome. I'm on Windows 8.1. It saved it to my download folder and when I double click on it, it opens Adobe Reader XI (updated) but only shows a totally grey or back document. If I go to Chrome and go to Downloads it open it ok in the browser window.

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