I haven't built that kit, so this is a guess. Were the silver layers supplied for all of the nat. insignias, or just the two one each side of the fuselage?
Maybe the idea is to be able to paint the stripes around the tail complete, then go back and add the silver in the places where the nat. insignia is. In the real case it was already there and the stripes got added, usually.
So there might be some area of silver around the bottom half of the insignia. No idea if that matches your alignment issue.
EDIT- looked at some online images of the decal sheet. Three out of four come with silver, the fourth being the wing top one where there weren't stripes.