One very strange side-effect of the change, at least on my system (XP), is that hotkey combos that include CTRL no longer work in some but not in all applications. Affected applications include BabelPad, OpenOffice and Firefox 4. Unaffected applications include NoteTab Pro, Atlantis (word processor), Archivarius, even Netscape 4.8!
This has been tested with the simplest of scripts, containing nothing more than this:
Which should give you a bullet when you type CTRL+SHIFT+B. In BabelPad, OpenOffice and Firefox 4 however, it either does nothing, or does whatever CTRL+SHIFT+B has been defined to do by the program itself (i.e. set the input language to Tibetan in BabelPad, or trigger subscript in OpenOffice)...
It looks like the affected programs are overriding AHK. Any ideas?