I am having a similar problem, although I do not have such a complex set-up.

I use mail-notification on my laptop, with an imap account and a gmail
account.
(note: the details of the imap account show the connection type as "in band
SSL/TLS".

Mail notification behaves fine until I unplug my ethernet connection.

shortly afterwards (i haven't measured the time - anyone know how i might?)
the cpu usage jumps to 100% until I kill the application. I think that it
takes longer than the mail account refresh period.

Running debian testing.
--------------------
Mail Notification version 3.0
Copyright (C) 2003-2006 Jean-Yves Lefort.

Mailbox backends:
 mbox                           yes
 mh                             yes
 Maildir                        yes
 POP3                           yes
 IMAP                           yes
 Gmail                          yes
 Evolution                      yes
 Sylpheed                       yes

POP3 and IMAP features:
 SSL/TLS                        no
 SASL                           yes
 IPv6                           yes

Sylpheed features:
 .sylpheed_mark locking         no

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