From Birnam Designs Wiki

Occasionally VMWare (I am using Workstation 6.5.1) apparently kills the modifier keys and a few others (Alt, Ctrl, Shift, capslock, etc.). The keys definitely still work, as they work fine in VMWare, but not in the linux host. e.g. Ctrl-a should do a "select all" but it just outputs 'a'. The ctrl key is definitely signalling something, as xev can see it. But it doesn't effect anything.

Running this command will fix the problem:

setxkbmap