It seems every time I install the patches, cometchat's urls are redirected. here are a few examples.

if I install cometchat I'll use the url www.xxx.com/cometchat/install.php the url is transformed to www.xxx.com/cometchat/installation/install.php this also happens to the admin url. when patches are on the chat box disapears, when I unpatch it comes back. Any help would be appreciated.

Versions:
joomla 1.7.1
Multisites 1.2.66

Now cusomer service is playing stupid because I sent a e-mail the same day my upgrades stopped. I have the emails, so if this is a matter of upgrading, I am entitled to an upgrade.

First cometchat is not a standard joomla extension as this extension does not save their data into the DB with the joomla table prefix but has its own unique prefix that forbid to have 2 websites into the same DB.

Second, the "installation/install.php" is a detection performed by joomla when it does not find the "configuration.php" in the deployed directory.
In this case, Joomla redirectory automatically the user to the current URL /installation/install.php to allow creating the DB.

Concerning the update of the product, see the FAQ for the procedure. It explains and show with video and PDF how to get a new download ID.
www.jms2win.com/en/faq/faq-joomla-multi-sites#cat-122