You might be seeing the affects of dithing with your signal. I'm not sure why it would be on one board, though not the other, one counter must be more sensitive. Anyway, dithering is caused by vibration or other outside forces that cause small glitches that add to the count total for the counter. There is a way around this, and that is to use a counte convertor. There is a page on this website that tells how to make one. The link is below. I would sugget trying this to see if it will fix the problem.
Brian
http://zone.ni.com/devzone/conceptd.nsf/2d17d611efb58b22862567a9006ffe76/6f25cba2cd73417786256869005e5fc3?OpenDocument