Here is some debuging output from the applet:

** (indicator-applet:6060): DEBUG: Building a new IM Menu Item
** (indicator-applet:6060): DEBUG: Building new IM Menu Item
** (indicator-applet:6060): DEBUG: Adding to IM Hash
** (indicator-applet:6060): DEBUG: Placing in Shell
** (indicator-applet:6060): DEBUG: Setting image to 'new'
** (indicator-applet:6060): DEBUG: Got Sender Information
** (indicator-applet:6060): DEBUG: Got Time info
** (indicator-applet:6060): DEBUG: Got Time info
** (indicator-applet:6060): DEBUG: Removing :1.127 2
** (indicator-applet:6060): DEBUG:      Comparing (:1.127 2) to (:1.127 2)
** (indicator-applet:6060): DEBUG: Got a message
** (indicator-applet:6060): DEBUG: Message subtype: email
** (indicator-applet:6060): DEBUG: Hmm, still no entries
** (indicator-applet:6060): DEBUG: Removing :1.82 0

** (indicator-applet:6060): WARNING **: We were asked to remove :1.82 0
but we didn't.

(indicator-applet:6060): libindicate-WARNING **: No indicator 0 of type
'message' on ':1.82'.

(indicator-applet:6060): libindicate-WARNING **: No indicator 0 of type
'message' on ':1.82'.

-- 
message indicator with pidgin seems to be flaky
https://bugs.launchpad.net/bugs/334349
You received this bug notification because you are a member of Indicator
Applet Developers, which is the registrant for Indicator Applet.

Status in Indicator Applet: New

Bug description:
I am seeing some flaky behavior in the message indicator, specifically with 
pidgin messages.  After starting pidgin, I do see messages that I receive in 
the indicator-applet.  However, at some point after running for a while I stop 
seeing incoming messages in the indicator-applet.  

I do continue to see notifications via notify-osd, and the indicator-applet 
lists both "Pidgin Instant Messenger" and "Evolution", but not specific 
incoming messages.  Restart pidgin makes it start behaving as expected again.

I am filing this bug against indicator-applet because I have seen this happen 
once with evolution as well, where restarting evolution resolved it.

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