What/who's flats are you using?
I have been using that same jig for years. I do remember having to hammer (soft head/dead blow) the flat on the bottom to square things up while still in the male jig, but everything else lines up great.
As far as the front/rear trunnion, how even are the cut upper rails where the trunnions slide in. If they are off (one side up/the other down), they can be uneven, and this will give you a uneven installation.
Also, from cutting the recess for the trunnions, if you haven't deburred the underside of the cut rail, that also can cause an uneven appearence.
I have been using that same jig for years. I do remember having to hammer (soft head/dead blow) the flat on the bottom to square things up while still in the male jig, but everything else lines up great.
As far as the front/rear trunnion, how even are the cut upper rails where the trunnions slide in. If they are off (one side up/the other down), they can be uneven, and this will give you a uneven installation.
Also, from cutting the recess for the trunnions, if you haven't deburred the underside of the cut rail, that also can cause an uneven appearence.