Today, I tried to update to the latest Groups version 3.2. I was using Groups 3.0 and wanted to upgrade to 3.2. If I move the files over but don't click update modules from the admin screen, everything works OK. Problem is if I click on update modules from the admin menu, the group tab is no longer on the header tab (it vanishes). It appears it is deleting the sql group entry from the Jcow_menu sql table.

I am not using version 5.0 I am using 4.4.

you have to be careful when updating the new updates when using 4.4. On the updated mods (groups, forum and pages) the install.php file lists the type of sql as "personal" in my opinion it should be "community" so it goes to you main panel. This caused me a lot of problems after I updated my modules. I fixed the issue though, I think.