A similar thing happened to me in my HG version, when I received the Pokemon into my part through GTS they would have 0 health, no stats and be at level 0. Although the Level health and stats where different from the pokegen file everything else was the same(such a species, nature, held item, attack and ect). What I do is deposit the Pokemon into the PC and then withdraw them and their stats, level and health was changed to what was set on pokegen, I don't know it happens like this but it really not much of a problem to me. This method worked for me, but remember that I'm using Heart-Gold so it maybe different.
Hope this helps.
