warp effect problem

What you are experiencing is the way the warp effect applies to shape layers.

It's not a glitch, it's just the way shape layers are affected by Warp.

I assume it has to do wth the way the dimensions of a shape layer are calculated vs the dimensions of the shapes on that layer.

If you just need to warp a rectangle you can use a Solid layer instead of a shape. 

If you have to use a shape layer you either need to pre–compose it or adjust the shapes position until yo uget the look you want.

Effects always operate relative to the layer and a shape layer is always the size of the composition. Your shape is not perfectly centered, so inevitably there's an offset. Adjust the position of the shape group for your rectangle. Also consider pre-composing your shapes to get predictable results.

Mylenium