This issue still occurs on 12.04. Sometimes, the only way to get it to work is to
killall pidgin and use the launcher from the dash. However, I came up with a solution that works every time.
Use the following command:
gksu gedit /usr/share/applications/pidgin.desktop (or use your favorite editor instead of gedit)
Add this to the bottom of the file and save:
[List Shortcut Group]
Name=Display Buddy List
What this does is an an option to the pidgin launcher called "Display Buddy List" that always will show the list whenever selected. But, if the list is showing already, it will not open a second one.
So, long story short, if opening Pidgin from the messaging menu gives you that trouble, use the solution listed here. Even if it doesn't work by clicking the messaging menu option or using the launcher from the Dash, this will always work.
Note: To those wondering why I didn't advice to copy the Pidgin launcher to
.local/share/applications, it is because the launcher in the messaging menu launches
/usr/share/applications/pidgin.desktop. So, rather than editing the messaging menu, I advised to edit the original launcher.