If you have a 1 inch to 1 1/8th shim it should fit snugly between the untightened stem (a 1 1/8) and exposed fork, no matter where it is centered underneath the stem. Ideally your shim should be around the identical length to your stem, but this doesn't matter much. If this is not happening, my best guess is that you have some funky shim or stem, which components are they? I have a thomson shim with a road stems and it works fine, maybe its your BMX stem?

And in case you are doing something wrong with the installation, I have the same setup and this is how I replace/adjust my stem. First you wanna slide in your spacers, followed by your stem with shim underneath, and top it off with the top cap with at least 2mm between the stem and edge of the fork. Once your stem is centered, tighten your top cap snugly compressing the headset/spacers/stem (important step, or else you will feel play in your fork). Then tighten your stem firmly, which really seals the deal, and finally I like to undo the top cap a little so its not under too much stress (Im paranoid about damaging the locknut). If you are doing all this correctly, then my best guess is that your shim and stem somehow are different measurements.