Welcome from NJ.
You could also try pressing your seams open vs to one side. I find my blocks lie flatter and things fit together better pressing open. I don't generally deal with pieces that small but it may help. And yes, the math says it should work out but it seems that the elusive 'scant' 1/4" seam is what is needed due to, as QuiltnNan says, thread taking up some of that seam allowance.
Good luck.