mintDesktop is a bad guess
That's an application that let's you configure your desktop and restore splash screens and the like....
enabling automatic login, with 30sec delay.
I may miss something but I thought the timed log in came with Felicia
Do you use the option Enable Timed Login in the Login window?
If you do or use "the normal" autologin there is a bug in X (may thus be solved in Felicia/Intrepid as there's a new version there)
A possible solution is
1. Right-click the keyboard indicator applet (I suppose you have this one when you have multiple layouts)
2. Select 'Keyboard preferences'
3. Select 'Layouts' tab and click 'Reset to defaults'. Check that all the configs are gone
4. Edit your xorg.conf file
Add two lines to your keyboard section:
Option "XkbLayout" "put the proper code* for your desired languages here"
Option "XkbOptions" "grp:alt_shift_toggle"
5. Save the conf
6. Reboot. The switching should work now with GDM autologin enabled.
*code = Mostly two characters like en for english I don't know the one for Czech