I have a master site with 2 slaves. I use the master site to update all content to the 2 slave sites with different themes. The menus are unique per site and have been working fine. For some odd reason, now menus are only being pulled from one site.

So for instance, the modules are still unique for each site and graphics, etc are not lost. But when using any menu module, it pulls the menu from only one site. And when I change a module to test it does change, but it changes all to that site's menus.

Joomla Multi Sites version: 1.2.19
Patches definition version: 1.2.25

It seems that they are linked or something, which is odd, because I don't believe I changed anything and this used to work correctly.

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I can tell which site menu item is being taken because the home copy and title reflects the site. For instance It would say, Welcome Slave1, on all sites.
The thing that is odd is that it changes From Slave1 to Slave2 every so often. I am going to stop messing with the site all together and refresh to see if it still does that.
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I don't think this is a permission issue, which is why I set it up separate and am going to close the other one.

well, I figured it out. I do believe it was a permission problem originally. I turned off the global cache and cleared cache. Then I made sure that the cache directories had the right permissions and the config files.

then I turned the cache on for each.