Don't forget that the VATS prevents ANY cranking, even with the bypass, for up to ten minutes after a "fault" or an attempt to use the wrong key. In your case, even if the key fits, the resistor chip must make good contact. If the VATS sees the no-contact scenario, but the key turns the cylinder, it will kill the fuel/starter systems for the duration; resetting the timer after each attempt.
When you try to crank, don't keep at it expecting it to go. Ten minute cooldown on VATS.