Okay, so I was confused here for a bit, simply because it appears that
(at least in Karmic) separate Prism processes are only separate if they
represent different applications or so and the task boundaries depend on
the INI file used to instantiate Prism.  For example, Prism will start
two processes for the following two commands because they are using
different INI files:

prism -override "/home/mbt/.webapps/google.ta...@prism.app/override.ini" 
-webapp google.ta...@prism.app
prism -override "/home/mbt/.webapps/launch...@prism.app/override.ini" -webapp 
launch...@prism.app

However, if you try to run either of those again while the first one is
running, the child process dies unexpectedly (from AllTray's point of
view) and there is nothing for it to grab onto; what Prism is doing is
instead sending a message of some sort to the first Prism instance, and
it then spawns a new window.  There is no way for AllTray to catch that.
(Note that in new versions of AllTray, such as in 0.7.4dev, the second
window will be caught by the first AllTray and it will use the same tray
icon and dock both, since it is a single application; however, that
version of AllTray does not yet have all the functionality of old
AllTray and it's not yet ready for general public usage.  I hope to make
a release soon that will be suitable for inclusion in distributions such
as Ubuntu and has all the features of "old AllTray", but I cannot yet
name a time when that will happen.)

It would seem that you can work around this if you use the Prism
application to create two separate INI files and then launch them both.
I'm not sure if that can be done the same way in Hardy as it is done on
Karmic, but if it is, you can do so by creating two desktop launchers
from the prism menu option (in Applications→Internet) and then open the
properties of the desktop file and use the commands that are there to
launch them.

I'm going to guess that this behavior is by design in Prism.  There
isn't anything that can be done in AllTray to fix that situation,
unfortunately.  I will, however, create a FAQ for AllTray in Launchpad
Questions so that at the very least the issue is known and there is a
workaround available generally.

** Changed in: alltray (Ubuntu)
       Status: Incomplete => Invalid

-- 
[Hardy] Cannot dock more than one Prism app using AllTray
https://bugs.launchpad.net/bugs/481186
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