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The stroke weight should be the same all around, unless you're doing something to the shape layer after the fact. The most likely cause is you've used a scale transformation on the shape layer. Be sure to create your shape by editing paths rather than using transformations, and check your shape layer scale has equal X and Y values.
Is there anyway to make the side strokes equal in weight when using the rectangle tool?
They already are. If not, then in addition to what Andrew said, you could also be working in a non-square comp withot using PAR correction.
Thanks for your help Andrew. I was exacerbating the problem by not editing paths; so that has been very helpful. The main problem was that I was drawing on a rectangular pixel comp.
Many thanks Mylenium; I was working on a rectangular pixel comp.