thanks fo the advice Joseph, it works well up to a point. I've managed to get rid of the unwanted underlining but unfortunately we use multiple background colors, e.g. text in side blocks is white on a black background while the main copy is black on a white background. As a result if I use a light color in the autoglossary values its hard to read one block of text and if I use a dark color you can't see the text on the other background.
What I really need is a way of forcing the text to stay the same color as the original style rather than changing it to a new color. I've tried setting it to color:none; but this didn't work.
Does anyone know if you can block autolinking to certain areas of text by putting something into the html code?