After spending the afternoon comparing the SEO Tool update against my other phpbb forum that installed 6.4 fine, i have spotted whats caused the issue.
Basically it was down to AutoMod getting carried away with itself and replacing to much code.
So for anyone else using AutoMod to install Ultimate SEO you may come across this so through would update
The PHPBB file affected was viewtopic_body.html in the template theme directory.
Line:- <a href="{U_VIEW_TOPIC}#p{postrow.POST_ID}">
This should have updated a line in between the below but replaced everything:-
<h3 <!-- IF postrow.S_FIRST_ROW -->class="first"<!-- ENDIF -->><!-- IF postrow.POST_ICON_IMG --><img src="{T_ICONS_PATH}{postrow.POST_ICON_IMG}" width="{postrow.POST_ICON_IMG_WIDTH}" height="{postrow.POST_ICON_IMG_HEIGHT}" alt="" /> <!-- ENDIF --><a href="{U_VIEW_TOPIC}#p{postrow.POST_ID}">{postrow.POST_SUBJECT}</a></h3>
also
Line:- - <a href="{U_VIEW_TOPIC}#wrap" class="top" title="{L_BACK_TO_TOP}">
This should have updated a line in between the below but replaced everything:-
<div class="back2top"><a href="{U_VIEW_TOPIC}#wrap" class="top" title="{L_BACK_TO_TOP}">{L_BACK_TO_TOP}</a></div>