Ok, as per description it is working pretty much exactly how it is supposed to save for health and spell points...the reason you get -2 total to saves etc is as follows...the spell itself gives you -1, then the -1 to effective level gives you -1. Your save at 13 was lower than your save at 14. Those two stack, the actual negative effect from the spell and the negative effect due to effective level.
Then as far as hp and spell points go I would be led to believe then that the enhancements and feats which have minimum levels or perhaps even attained at levels you higher than your effective level would be neutralized...on that however I'm not sure. But the -2 makes sense to me.