Won't be the capacitor, no - that doesn't get in the way of the head of the centre screw for the contact breaker. The risk is the other way - ie if the centre screw touches the earthed side of the capacitor, the magneto won't work
If the magneto's main earth brush isn't functioning for some reason you may in some circs get a shock, or see sparks off the screw when you earth it, as the earth brush's job is to provide a return path for the HT current. As Trevinoz says, best check it's working.
I'd give the head of the centre screw a good clean, check there is continuity between the wire off the end cover and the brush or pad inside it that is supposed to touch the screw, and that there is permanent contact between the two. It's odd that a direct link from screw head to frame doesn't stop it, but these things can be sensitive sometimes.
