Try putting up different tolerances with - sign (like symmetrical or both negative tol. values) and check?
Also check if it is same with a word file.
Try changing the font of the dimension and see if that does it.
Also check if it is the same result when using something else then the built in PDF function.
E.g. : PDF 995 or PDF Creator.
The reason I mention that is when the built-in one doesn't give WYSIWYG results then other PDF programs do give a good result.