I agree that this is the formula for making HST and I add 1" and trim. Before I trim however I sew 1/4" on both sides of the diagonal line. I don't see where you are making HST but it seems rather you are adding the cut triangle to the square. I'm also confused about your comment that you trim two sides. If you are making HST using the mentioned formula you trim 4 sides unless you have the Quilt in a Day ruler which you trim a folded HST on two sides.
A picture would really help of the quilt and the pieces in question. There are too many unknowns in your description to be able to answer. I'd like to help but I'm confused.