Hi Kevin,
I have seen behaviour similar to what you are running into if 'Large Fonts' is turned on through the Windows display properties. If you have either this or the Scaled fonts enabled in Windows, try disabling this and print/preview checks - perhaps in sample data.
In the specification itself, the page height is determined by which sections you have selected, the height of each of those sections, and the 'Max Details' setting found in Specification Options.
You do not have to use a separate check spec for manual checks than you do for system checks. If you are finding that System Checks are OK whereas Manual checks do not, I would not suspect the check spec as the culprit.