Soft buttons disappeared
There is a mode in CyanogenMod and other ROMs called "Expanded Desktop". If your phone is in Expanded Desktop mode, then the navbar will not be visible (The notification bar may also be hidden, depending on your settings).

The easiest way to check if you're in Expanded Desktop is to try toggling it. Simply long-press the power button to get CyanogenMod's expanded power menu, then tap "Expanded Desktop" to toggle it.

If your buttons showed up after doing this, then you're set! If not, it's something else.