Even though it's been four years, I would definitely contact the company that produced the mat. Just tell them the problem, as you've explained it to us. Anything that's sold with marked measurements, is bought under the assumption that those measurements are correct. If the measurements are noticeably off, then the mat is defective.
That said, I also use a ruler for my final measuring. Although my own (Olfa) mat has proven to be accurate enough, my habit of measuring from the exact same center point of each line, is not.
I used my June Tailor Shape Cut ruler, for accurate blocks.
http://www.junetailor.com/shapecutvideo.htm