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I don't follow why you had to change the original webmaster usergroup - but I haven't used phpwiki, so might just be me.
Some things are hard-coded, such as the define("XOOPS_GROUP_ADMIN", "1");
define("XOOPS_GROUP_USERS", "2"); define("XOOPS_GROUP_ANONYMOUS", "3");
in the mainfile.php.
This has helped a lot of people, who accidently removed system admin access to the webmasters group and thus saw the Administration Menu link disappear from their user menu. By typing the direct url to the admin module, members of the (original) webmaster group can then resolve the problem without having to reinstall XOOPS.
I guess that can be changed if you really want... but I'd rather do something about that phpwiki module.