Upgrading my system to Ubuntu 9.04 x86_64 (pidgin 1:2.5.5-1ubuntu8) has fixed the problem for me.
To be specific: I can now uncheck "Mute Sounds" and Pidgin will play a happy "do-DOO" sound when it starts up and (automatically) logs into to Freenode.
It's entirely possible that it was not the upgrade to pidgin but something else (maybe Evolution, as raccoonone suggests) that fixed this problem.
Upgrading my system to Ubuntu 9.04 x86_64 (pidgin 1:2.5.5-1ubuntu8) has fixed the problem for me.
To be specific: I can now uncheck "Mute Sounds" and Pidgin will play a happy "do-DOO" sound when it starts up and (automatically) logs into to Freenode.
It's entirely possible that it was not the upgrade to pidgin but something else (maybe Evolution, as raccoonone suggests) that fixed this problem.