Question #25156 on pidgin in ubuntu changed:
https://answers.launchpad.net/ubuntu/+source/pidgin/+question/25156

thingymebob proposed the following answer:
pidgin 2.5 also has this in ubuntu looks similar to this debian bug
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=434089
(Buddy list synchronization issue in <foo> not handled correctly. In a certain 
state the message "Buddy list synchronization issue in ..." can popup with at 
least an MSN account. Two choices are given. Choosing _either_ does not resolve 
the issue, since after a restart of pidgin the same message pops up again. 

So, the problem is that Pidgin detects a problem, claims to have two
possible solutions, but none of the offered solutions are effective. )

Certainly linked with pidgin Evolution plugin. To recreate enable
evolution plugin, sync contacts, disable evolution plugin restart pidgin

Deleting the ~/.purple folder works. Also backup the accounts.xml file
so as you don't have to set them all up again

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