I can confirm this behaviour. It seems to be at least partly related to bug #58083 - after installing a fixed xserver-xorg-core-package, that is one where XkbGetKeyboard-function is fixed, the problem vanished.
** Changed in: gnome-applets (Ubuntu)
Status: Unconfirmed => Confirmed
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Keyboard Indicator applet does not show correct text after a second login
https://launchpad.net/bugs/76011
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