i can't tell you how many times i've had to re-lace a wheel because i laced it wrong. it surprises me how many different ways i can screw it up if i'm not paying attention . sometimes it shows the symptoms you've described, i've rarely bought spokes of the wrong length due to miscalculation, but i'm sure it's possible though.

if i use spoke length software off the internet, and i do, i usually get a "second opinion" from a second internet site. and see how they compare.