>When using a base href in a page, if you link a link to an internal anchor, as you have a base href, this will make the internal anchor to be searched from the base href location and not within the current document. Anyone found a workaround for that in the syntax of the A HREF tag?

The base href only affects relative URI's, what you need to do is give an absolute URI as the href. The following may work :

<a href="" onclick="this.href=document.location+'#localanchor'">Local Link</a>
...
...
<a name="localanchor">