OK - I looked at both your PDF and PSD files and the dot pitch (spacing) is, as you said, 0.125 inch in both of them. However, I noticed that your ppi was set to only 72 pixels per inch. This is extremely low for printing. If printed at this resolution your dots/crosses will be clearly pixelated.
The 1st possibility I can think of is that this may have something to do with your problem. For example, to get your dots to not show visible pixelation, the printer almost certainly will up-rez your image to at least 200 ppi, maybe more. If he is not aware that you need exact scaling, he may have done this in a way that does keep your dot spacing exactly constant. You will have to discuss this with him.
The 2nd possibility that I can think of is that the printer he uses may have non-printable margins, so he may have scaled your image so that it fits the printable area which is slightly smaller than the size you expected. You may already know about such matters, but there is a nice Wikipedia article on this:
http://en.wikipedia.org/wiki/Bleed_%28printing%29. Again, you will have to discuss this with your printer.
HTH,
T
PS - Pls. keep us posted if you find out anything or have other questions.