I am pretty sure that WoW handles its own keyboard input in a slightly shaky way. Guildmates are reporting 'stuck' keys, such as modifier keys or just normal keys - and they are not boxing, just one account, one pc, no frills.

Usually the trick is to push the offending button again while having the WoW window focussed, thereby creating a key pressed and a key released event, which hopefully gets rid of the key down state for WoW.

This may happen more often with alt-tabbing, switching one keyboard between systems with software or hardware solutions, but it does happen even without any multiboxing.