Omer is right, this cannot be a bug in xchat.

Unfortunately, I can't reproduce it. I've tried getting two versions of
the same program into the menu by

* quickly exiting and restarting the program (manually, and from a terminal)
* starting the program more than once (this works for xchat)
* adding a file in ~/.config/indicators/messages/applications that contains the 
path to the app's desktop file

Looking at the code, it clearly tries to avoid showing the same
application twice (src/messages-service.c:1384 ff.).

I've also not succeeded in getting an application show up after the "Clear" 
item. This commit tries to make sure this can't happen:
------------------------------------------------------------
revno: 217.1.14
committer: Ted Gould <t...@gould.cx>
branch nick: clear-notifications
timestamp: Fri 2011-07-22 12:15:00 -0500
message:
  Make sure clear attention stays at the end

Maybe that commit wasn't yet released into 11.10 when Matthew reported
this bug?

Please feel free to reopen this bug if you find a way to reproduce it,
or it still happens on your machine.

** Changed in: indicator-messages
     Assignee: (unassigned) => Lars Uebernickel (larsu)

** Changed in: xchat (Ubuntu)
       Status: New => Invalid

** Changed in: indicator-messages
       Status: Confirmed => Incomplete

** Changed in: indicator-messages (Ubuntu)
       Status: Confirmed => Incomplete

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https://bugs.launchpad.net/bugs/856284

Title:
  Application shown twice, before and after "Clear" item

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