unbind everything, and set it all back to defaults.
Then check what e does. It should be bound to the call for medic command (cant remember what the exact command is off the top of my head)
correct! however it also changes teamdisguise as a spy

Is this only while you have the diguise pack *thingy* out? so as a spy at any other time (disguise pack not out) you can call for medic successfully?
My E button is scripted to call for medic twice (for all classes) so in essence a custom command. I will see later (when home) if I too can change disguiseteam with the E button, while as spy.
My gut instinct is that this is now a bug, and should be reported to valve through the in game 'report bug' menu.
EDIT: if this is the case, as a workaround you will need to use different keys...