I fixed the issue. It turned out that the issue was unrelated. I was parsing the html into a xmldoc and this was stripping the . I had to do some manipulation to prevent it.
However, my other issue is still unresolved - I have version 5.0, so the properties window is different from that in 5.2. I downloaded the version in 5.2 and saw it, then I figured out why you dont see what I do. In the version 5.2, in the stylebuilder, the font color and highlight color have the color picklist, but thats not populated in the version5.0. Morever, and this exists in 5.2 as well, if you type in the color, you get a javascript error. If you paste the color in all at once, this doesnt exist.