As far as I know, spell files can only effect you from being able to get a character in game from character select, not anything to do with logging into the Login Server. Though, I think it would be possible to add something to block people from being able to connect to a particular server in the server list if a certain spell file wasn't used, but EQEmu doesn't support a feature like that yet.
As for issues with the official EQEmu LS, it is hard to say. It could be any number of things. Since Rogean is the only one with access to it currently, he may be the best one to help in support of it. The only client related issues that might cause something like that as far as I know is if you have patched to Live at all, or if you have ports blocked on your network or ISP.
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