I have been facing this same problem for the past year and have tried about everything I can think of. Please, someone help us! Similar problem with java, too... Have shut down protected mode, have uninstalled and re-installed, made sure "enabled" is checked in the Security-Custom area (tools). Have wasted time and still face the same annoyances.
We've tried so many things it's hard to determine what's worked. But - the last we did was to follow the uninstall intructions on http://helpx.adobe.com/flash-player/kb/uninstall-flash-player-windows.html. In brief, we deleted all the files and folders within our FlashPlayer32 folder (subfolders and a list of files). We then reinstalled (for us, too, easily the 20th time we've reinstalled over the past weeks/months).
The resuilt of the above. No visible change! Still did not work.
BUT - we then hit upon another instruction, whose wording did NOT match our IE tool-bar options. But - following the gist, we went to Tools - Internet Options - Security - Custom - and Disabled ActiveX Filtering.
Low and behold - Flash Player suddenly works! Why? Not the faintest idea, given that on our other laptop, and our desktop, Flash has always worked with no problem, with ActiveX Filtering enabled. Now - we'll see if we've spawned other nifty problems as a result of the above "disable"!