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Hi Deepy, and Everyone.
Yes I found that out after many times screaming at my PC.
When I had the Groups permissions tables shared, site1 worked okay, but when I went onto site2, site2 had some modules working which had not been installed in site2, and when I went into the group permissions and removed them, they removed okay and site2 was now working. Which made me happy.
But when I logged back into site1, the modules I removed in site2 did not show, so I went into the group permission, and put them back, I spent a good 2 hours going round in circles.
So I found it better not to share the Group tables, as my sites don't always have the same modules installed, so now by not sharing the group tables, I can now install a module in site2, and set the permissions for site2, and the tables for site1 stay as they are set for site1.
And like I said before, before changing anything in the shared tables, always backup your database, as you can spend 4 hours working on your site getting it to work, and one simple mistake can in just 1 min, can cause you a whole load of pain when your sites stop working.