Hi,
I have JMS 1.2.19 on Joomla 1.5.15
Here is the issue:
SH404 uses URL cache in components/com_sh404sef/cache/shCacheContent.php
This is the single file handling all the url cache and thus there is overlap of article/category/section ids.
Here is a sample file for reference.
// shCache : URL cache file for sh404SEF
//1.5.4.302 - <a href="
dev.anything-digital.com/sh404SEF/".../sh404SEF/</a>
if (!defined('_JEXEC')) die('Direct Access to this location is not allowed.');
$shURLCacheCreationDate = 1264422342;
$shURLDiskCache[0]='index.php?option=com_content&Itemid=3&format=feed&id=1&lang=en&layout=blog&type=rss&view=section#section1/feed/rss.html#0';
$shURLDiskCache[1]='index.php?option=com_content&Itemid=3&format=feed&id=1&lang=en&layout=blog&type=atom&view=section#section/feed/atom.html#0';
$shURLDiskCache[2]='index.php?option=com_content&Itemid=3&id=1&lang=en&layout=default&view=category#category1/#0';
$shURLDiskCache[3]='index.php?option=com_content&Itemid=3&catid=1&id=3&lang=en&view=article#article1-alias.html#0';
$shURLDiskCache[4]='index.php?option=com_content&Itemid=3&catid=1&id=1&lang=en&view=article#article2-alias.html#0';
As you can see it creates common cache file for all sites without any reference to the originating site thus the first site to register its id gets the url listed and the rest of the sites get that data.
I hope its clear... If not let me know.