You can fix this by either going into the "trainer.ini" file or in-game.
TRAINER.INI:
Note: You can open *.ini files with a text editor, such as WordPad, Microsoft Word, or the most used NotePad and NotePad++. NotePad++ represents most coding bunches but to be honest, it doesn't really matter, it's your preference.
Open up your "trainer.ini" file and look into it.
You must edit a line in the "////DEFAULTS SECTION////".
Replace the line
KeyBindingsDisabled=0 //Key Bindings (except menu keys) disabled on startup
with
KeyBindingsDisabled=1 //Key Bindings (except menu keys) disabled on startup
Or, you can replace your "trainer.ini" file's text with this.
INGAME:
By going to "Options" page 1, near the end, on the right side of your screen, there is a line that says "Enable/Disable Keys", and toggle that. Note this is temporary, aside from a permanent on-start change with the "trainer.ini" method.
Regards.