Blocked

So, this is going to sound funny, but I can't figure out my villain. I LOVE my recent story. Love the heroes, love how they save the day at the end (yes, I even have that figured out), but I just can't figure out WHY my villain does what he does. Kind of a problem, don't you think?
I had this problem with my last book too. My villain was a crazy mad-scientist type who was simply out to get anybody with more power than him. BORING. Somebody suggested to me (at a Writer's Conference-- another plug for those) that I write a short story about my villain to flesh him out. So I did, and suddenly I found out what his motivation was. He didn't start out bad, just very smart and very vain. But his lab assistant, someone who he disdained as weak and emotional because she had a crush on him, used her unique abilities to overpower him and turn him essentially into a slave for years. The experience humiliated him, robbed him of his free will, and his ability to rise to fame and fortune. He hardened (I'm a little vague with the details in case it ever does get published some day). His fate as a villain was sealed when he killed his captor and escaped, swearing vengeance against anyone who had the same abilities, and yet desperately longing for those abilities himself (there may be even better ideas out there, but this one was WAY better than what I started with).
Now I've come to a roadblock again. What is this villain's motivation? Power and control always seem to be what villains want, it's the WHY that matters I think. Why are they willing to do things that other people aren't in their pursuit of power? What happened to twist them, to make them unable to feel empathy or sorrow for their victims? Certainly they must be uniquely gifted. They must have some sort of special capacity that will draw people to them, give other bad guys a reason to follow them. They must be leaders. And there must also be a legitimate reason why the good guys haven't been able to overpower them. I hate stories when there's this super villain who through the whole story is causing all sorts of trouble, and yet in the end all it takes is one small thing to defeat them (I like the Wizard of Oz, but the ending always bothered me. Sorry for those of you who love it, but seriously, if the wicked witch could be killed with a splash of water, WHY would she leave buckets full of it just lying around her castle? And did she ever have to run to get out of the rain? Did she never bathe? What about sweat, or drinking water? A water allergy seems like a pretty huge impediment to super-villainy.)
Anyway, these are the things that I have to work out. How can I possibly have a story without having my bad guy already worked out? I can't. So until I think of something compelling, I've stopped working on my manuscript and started working more on the world my story takes place in. The story behind the story.