I thought I would play with this too, when I ran a UBB Treads board it had the cool flashing mail icon (it's animated) and I missed that so I added it back with a simple conditional.
Find this section:
PHP Code:
2="$vbphrase[total_x_nav_compiled]" 3="$session[sessionurl]">$vbphrase[private_messages_nav]</phrase></if>
</div>
</td>
Add this right under:
PHP Code:
<if condition="$bbuserinfo['pmunread']">
Your blinking image or whatever goes here
</if>