I believe that [VT Switching](https://dvdhrm.wordpress.com/2013/08/24/how-vt-switching-works/) has little to do with keyboard layout. It involves kernel hard-coded shortcuts and also Xorg configuration.
Assuming that you didn’t touch the kernel I would say that this is an Xorg issue but honestly I can’t point you to anything more accurate.
If I were you I would start diagnosing the problem in this way:
1) I would boot in “init 3” and then I would try to see if the VT shortcuts work properly
2) I would load X or mdm (service mdm start) and I would try again the VT shortcuts.
If they don’t work anymore then the research field is narrowed to:
A) some kind of X mis-configuration (watch out: most of the documentation available about X is outdated)
B) some cinnamon mis-configuration.
I would then start looking around the cinnamon control panel (B), parsing every single item of the keyboard configuration panel (don’t rush, it’s quite extended). If nothing comes out I would definitely go digging what’s wrong with X.