Sometime in the last couple of months (sorry for the vagueness), Claws auto account selection on compose broke. I've just tested the current git version with a virginal config file, and the problem still exists. It always defaults to the first (of two, in my case) account listed.
I just raised that question on the list recently. Compose now also uses the account selected in the lower right corner of the Claws window. You can configure a default compose account per folder though by right-clicking a folder, selecting "Properties..." for the context menu, switch to tab "Compose" and then select a default account in there. See also: http://lists.claws-mail.org/pipermail/users/2016-April/016193.html
I'm confused. What's the purpose of Configuration > Preferences... > Compose > Writing > Automatic Account Selection then? I preferred the way it worked before :(