Hello,
some thoughts:
1.) Dave Yeos tip is the best. Makes sense and do that. Eventually delete any master.passwd, pwd.db and spwd.db before installing.
2.) Rich Walshs tip is ok, too. However Samba not requiring master.passwd et al maybe be technically correct, but not a good idea. It is however completely wrong that the GUI tools impose the usage of the *nix password database. It is the Samba core that requires the *nix password/user database for certain operations (not all).
The whole philosophy of Samba and it companions (and basically this is exactly the same with *nix) is to keep the *nix user/pssword database and the one from Samba synchronized.
In case the synchronization is lost (for example due to manual modifications), things start getting in any degree from strange, weird, to absolutely non functional. Your mileage may vary. Getting the 2 asynchronous databases back to sync again is (almost) impossible.
3.) SSCC (Simple Samba Configuration Center) does not come with a master.passwd because it creates it from scratch in case none is found.
4.) The error you see when logging into Samba Users and Groups is interesting. It is obviously unable to parse something very weird. I'd like to know what and will try to provide a fix for that. Your problem is however likely the one described in item 2.) last paragraph.