However, my CD (x64) (now installed into C:\Program Files) still does not recognise 64-bit programs that also install by default into C:\Program Files (rather than C:\Program Files (x86)). My workaround is to install 64-bit programs into my C:\Program Files (alt) folder, but surely I shouldn't have to do that now?
Are you talking about Circle Dock or StandaloneStack (which powers the Stack Folders) as not recognising your Program Files folder? I suspect the latter which, as it is a 32-bit program, will be redirected by the OS (regardless of your wishes!) to the 32-bit equivalent folder. Not a lot I can do about that, I'm afraid, as I'm not the author of StandaloneStack.exe or its Docklet library files.
Also, CD is still a bit hit and miss as to whether it picks up program icons, and for a couple it displays just a "blank" icon - but the programs launch so I can live with that.
Circle Dock will try to locate a usable icon image from within an executable's resources. But not all authors place much more than a 16x16 pixel icon there which is the smallest Windows allows for - that icon size, incidentally, has been the same since Windows v1. Circle Dock won't use a 16x16 image because it's simply too small to use on a dock which typically has 48x48 pixel images and an image enlarged by that large factor will look pretty horrible.
If you don't want to use our default, you can find thousands of suitable images on a number of web sites - including Rocket Dock's image library which our Help Browser opens automatically. Failing that, Google is your friend.
Apart from these small gripes CD is an even better program and I love using it.