I thought I was going crazy the other day when it stopped working.
I run two wow's on two machines, and normally I send to "World of Warcraft" on the second machine so I don't need to bother renaming windows.

What seems to happen is that the actual "World of Warcraft" window isn't being recognized. If you put up another window with the "World of Warcraft" title, such as a website, your keystrokes will be sent there. However if the game window is the only titled window matching "World of Warcraft" the keypresses go into the void.

What I found to work was to manually rename my "World of Warcraft" default window to something else and direct the script on my master hotkey client to send to the new name, and not "World of Warcraft."

Hotkeynet simply can't recognize the default "World of Warcraft" window.