That's a generic OS X (mis?)feature. The OS tries to detect when an app is already open, and forward you to the existing instance rather than starting a new one. You can see this behavior spreading into other apps like firefox which try to prevent multiple instances even on other platforms.
Anyway, try "open -n /Applications/Aquamacs\ Emacs.app" on the command line (e.g. in Terminal.app). I'm not sure whether a gui equivalent exists.