Should be related to your navbar template. Go to
Style Manager -> Your Style -> Navigation / Breadcrumbs Templates -> navbar. Check where your register link is being generated. Check if it's similar to this:
HTML Code:
<if condition="$show['registerbutton']">
<td class="vbmenu_control"><a href="register.php$session[sessionurl_q]" rel="nofollow">$vbphrase[register]</a></td>
</if>
If it's not similar, make sure the entire line of register.php and onward is right. Does that fix your issue?