It doesn't matter what your seam allowance is! What is most important is the size of the blocks (and units) as you stitch them!
If you are making HSTs that finish at 2", after your diagonal seam is stitched it should measure 2-1/2" x 2-1/2".
If your directions call for scant 1/4" they are probably allowing for the slight amount of fabric taken up as you press your seam allowance to one side. Is it possible to contact the person who wrote the directions to ask?
If you want to check to see how accurate your seam allowance is you might want to try my seam allowance test. Check it out here:
http://good-times.webshots.com/album/569415726bHNKHF