Yea it does seem pretty wierd, but Enhancing does Affect how long Regen lasts, Refresh too, and things like the Bar spells and their efficientcy of resisting things. So thats plenty a reason for me.
Another thought might be the potentcy of Shell/Protect, try buffing yourself with ProtectI and then check you Defense. Come back a few lvls later and try it again. See if it has gone up with your Enhancing lvls. Its hard to check Shell because there isnt any marker, but you can test that by getting some monster to cast Aeroga on you with and without shell to see. Remember Shell is a GENERAL and Generic type of magic elemental defense. You can also try putting shell on and let a gobbie throw a bomb, and try a bomb throw without shell to see.
EDIT: I also wonder if the MND of the person your casting on matters..but i aint sure
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