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Cannot reproduce, those keys work fine in all four combinations for me. (4.x cli, 4.x aterm, 5.x cli, 5.x aterm).Probably Virtualbox's fault. Could even be that it's some hotkey used by vbox? Perhaps you used older vbox for 2.x, etc?
I just tryed and got the same results as OP.Aterm and 'console' do not react to keybord input.URxvt inserts the letter ä but does still react to keybord input.kmap=qwertz/de-latin1kmap=qwertz/de-latin1-nodeadkeys
Are you using vbox kernel modules or not?