I'm using E17, and claws will always iconify (minimize) when I restart E17. I do not use any plugins, and I have not been able to find any config settings to disable this behavior.
This may well be fixed in latest CVS in which I've fixed related issues for Gnome Shell. Could you test it ? We even have snapshots at http://www.claws-mail.org/snapshots/ :)
Ah, excellent! I have tried the latest snapshot and can confirm that this is indeed fixed. I am closing the bug :)