Go with the Manufacturers recommended refresh rate. It will have it in the Technical section of the PDF Manual or Booklet your fiend got with the monitor. My TFT is the HP Pavilion f1703 and the refresh rate is 60hz. Flat screens are made primarily for office use in fluorescent or incandescent lighting and there is no need for filters.
we need to be cetain of what you mean by "Flat screen". CRT monitors with a flat screen will cause headaches if the refresh rate is lower than 75Hz (it's not mhz), and some people - me included - think that it should be at least 85hz.
Many people refer to TFT monitors as 'flat screens', and if this is what you mean then the headache is not likely to be the result of a low refresh rate - such monitors will almost certainly be preset to at least 75hz. These monitors are unlikely to cause headaches, but they aren't necessarily 'better'than CRT monitors - in fact graphics professionals tend to prefer a CRT for its better colour rendition.
Whichever type you mean, the headache may be caused by an over-bright screen,or one which doesn't have the contrast setting high enough in a brightly lit room. Bad posture - resulting from an uncomfortable chair is a major cause of headaches and neck pains.
In any event, I wouldn't think that a screen filter would have any beneficial effect at all.