Can Popup alerts be disabled?

Alerts that appear in popup windows can be very annoying.
For example, I use IMAP server which is checked every 2 minutes. But to 
access this server I must be on VPN connection. When I use regular 
Internet connection alerts are just popping up saying that Thunderbird 
Failed to connect to the server. Like really big deal and I need to stop 
what ever I was doing and click Ok on that window.
It really should only display this warning in the Status Bar and 
eventually log it in some log.
Is there a way to disable these Popuping-annoying alerts?
If not then I really think that it should be in next release.
I think that popup window alerts should be removed from Firefox too. 
Firefox could simply display what ever it wanted to display as a Page, 
similarly to IE.
I think that Popoup windows should only appear in 'catastrophic' 
occasions like browser crash and similar.

Thanks,
Stefan