That usually means they aren't grounded properly. Look carefully over all the ground points.
Or, the caps are shorted or are the wrong value. Such as .47 instead of .047. Check grounds, check that a bare ground wire, (like the one that goes to the trem), isn't touching something when the pickguard is lowered into the cavity.
Also, is the control cavity shielded? Look for indentations to see if the 5-way is pushing down into the shield.
With the pickguard leaning out, tap on the pups and operate the tone controls. If they affect the "tap", then something is touching when you lower it into the control cavity.