Hotkeynet stopped working

[r3tardbatman]

My money is on Blizzard having done something, I'd bet there was some kind of patch this morning in combination with the maintenance.
Using hotkeynet I can control both Half-Life 2 & The Stanley Parable, as well as enter text in chrome. With WoW however I can't do more than rename the windows. Thus it's not something that's changed in Windows that's broken it.
I'm running Windows 7 Ultimate, last update received March 16'th. Tried disabling my antivirus which did nothing and I'm about to fire up my other computer in safe mode to see what happens there.

EDIT: CKS does work however, unfortunately it's not exactly a substitute.