As per the instructions in Semantic's INSTALL file:
Edit the file [wikipath]/includes/Parser.php. Insert the line
wfRunHooks( 'InternalParseBeforeLinks', array( &$this, &$text, null ) );
in the method "internalParse" right after the line
$text = $this->replaceVariables( $text, $args );
This is the only hack required for full functionality of Semantic MW -
everything else is already achievable with existing hooks.
I will attach a patch shortly (from revision 20529).