Links builds static HTML pages when you use the build function in the admin (except for search, add, modify, and the email/newsletter subscribe screen). If it only happens once in a while, you are probably having a problem with some of your builds. Perhaps trying the staggered build will help???

The only way I can see the CSS tags causing this problem is if they have somehow been moved to the same line as one of the <%if...%> or <%endif%> statements. You could double check to be sure, but if it only happens sometimes, it's not too likely to be the culprit. Otherwise, the CSS shouldn't affect page building at all (only final rendering by the browser of the fully built page).

Just FYI:
Doc type declarations don't (currently) affect page output or browser rendering--it's used by HTML validators to check for errors.