I used a stylesheet to add documentation to 100s of XSD files.  An example of
what one looks like:

...
> This is all well and good, but when I run a simple

javadoc ant target, which builds itself from comments made in the code, the
html that is generated comes out like this:

The java comments are perfect.

It seems you generate Java code from the XSD files. If the JavaDoc
comments in the generated Java files indeed look good, this is
really more a JavaDoc question. It may alos be an issue with your
Java generator. You better ask on a list with more expertise in
either of the above topics.