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Anybody know why we shouldn't do that? It works just fine (had to change it once I read the warning though), and I'm not sure why they don't want it used that way.
session_register() only works with register_globals on and is thus deprecated along with register_globals. You shouldn't have to use either it or session_is_registered() etc. any more as $_SESSION and isset() do the job better.
To answer the specific question though - generally $_SESSION and the old session functions don't play nicely together and normally if you use both the sessions won't work.