I've got a multisite setup on D6.4. We had some modules that were in sites/all/modules but decided we wanted to isolate them in the main site, so I moved them to sites/specific_site/modules. But they dropped out of the modules list on admin/build/modules and the system table pathname was not updated. Even if I manually edit the pathname in the systems table, they do not show up. Move the modules back to sites/all/modules and they show up again.
Initially this was with ubercart, but I also tried it with pathauto to make sure that it wasn't related to being a large group of modules. Same behavior.
The sites/specific_site/modules does have other modules in it that are being found and used, but I don't seem to be able to move modules there from sites/all/modules. I even tried deleting the relevant entries for the modules in {system} thinking that Drupal would find them as a new installation, but it still doesn't find them in the specific files modules folder. I never ran uninstall on anything (I don't want to lose all those ubercart config settings), and I've got a dedicated host account.
Any ideas?