Ok, let me see if I can try to explain it. If you specify pixels in your CSS file, as in 12px, users on Internet Explorer can't scale fonts up, which they tend to do if they are on a laptop or high resolution setup. In order for the scale up function to work properly, you need to specify percentage (as in font-size: 100%), em units (font-size: 1em) or a relative size such as small, medium, large, etc. The problem of course becomes the fact that if you do this, you have very little control of the appearance of your site.
I, for one, am very particular how my sites look, so I specify pixels. Based on the percentages of visitors to my sites, I will vary this size accordingly, but I have found that well over 75% of the visitors are on 1024x768 resolution in IE 6. For them, 12px looks just fine.
If you want to get really precise, you can use a detection script to deliver different style sheets for different resolutions. However, simply specifying a percentage or an em value for fonts will allow the user more control over how the site looks, and should help you to solve your problem. Just don't expect it to look great when the user sets the font size to display as large
Test out the different options and view it in different resolutions and see how it looks.