I just moved the program folder into Programs and it works fine. Why installing PepperFlash on Chromium in Windows has to be such a pain is beyond me.
So I get Adobe pepper flash beta 16 running on Chromium and go to a site with flash. Pop up says flash is outdated and to download version 15 the regular flash version. I had to install Chrome again and strip pepperflash out of that and add a string to the shortcut but now I have it.
I used to download Chromium from here http://chromium.woolyss.com/ and they also have a flash download directing to adobe, but some sites tell your on old flash when you are on a beta http://chromium.woolyss.com/#flash Have you tried using the flash version switch?