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Just today I have updated Flash from Adobe, installing the "regular" version instead of that "Square" thing, already tested it and it works fine.
Download Adobe - Products : Adobe Shockwave Player as well if you don't have it, then start IE again, click on the gear icon -> Manage add-ons and see if flash+shockwave is Enabled. I'm afraid that's all the help I can provide for now, as I never used 64bit in my life.
EDIT- from your screenshots, it's definitely Flash. Uninstall "square" and try to download the regular version + Shokwave.
Ok when installing the shockwave player should I install the full or slim version and should I install ActiveX or EXE?
Ok thanks. Any idea whether I should go with the slim or full install?
Try full.
If the problems persist, you can reinstall IE, or just click the gear icon, go to Internet Options -> Advanced -> reset IE. If you already set up bookmarks and feeds, don't check "delete personal settings".
Ok so I uninstalled all of the adobe software and reinstalled the 64-bit flash and now everything seems to be working properly excpet for websites wanting to run the shockwave flash b/c I haven't installed it again yet. Thanks
For me everything is fine except the favicon in the tabs: in my favorites it's ok but in tabs it's the IE icon.
I can only assume that you haven't cached the web pages completely/logged in or something, I didn't experience any issues with favicons, apart from the old problem in IE8 not recognizing some favicons at all, even though they are displayed in other browsers.