I had been having trouble adjusting the rear derailleur on my Kona Caldera I won at an auction a couple weekends back. Turns out the derailleur hanger was bent. I removed the hanger from the bike, put it in a vise, and straightened it out with a wrench. But now, when I close the skewer, the hanger is flexed towards the wheel, and in turn misaligns the derailleur. So, what can I do about this?

do it the right way. install wheel with skewer clamped. then use a hanger alignment tool

...or if you haven't got the tool, take it to your LBS.

if the hanger has a good bend in it i like to use an adjustable wrench or my knipex pliers wrench to eyeball it first. the hole can stretch or wallow out if its bent pretty good.

Or get a new hanger. Maybe it's not supposed to be completely straight or you somehow distorted it while attempting to fix it.

The problem is that your dropouts are not parallel. Your skewer makes them parallel, but only temporarily. This stresses the axle.

Fix the dropouts first. Then align the derailleur hanger.

Thank you all for the help so far. I guess if I can fit it, it would be cheaper to buy a new hanger than to have the LBS fix it.

....That was not what I was hoping to hear

What makes you think the dropouts aren't parallel? It looks to be only the hanger moving.

The hanger moves because the dropouts are not parallel. I can't think of anything else that would cause that.

Your LBS can do both of these alignments for a total of about $10 to $20. It's totally worth it. The dropout tools are $85, and the hanger tool is almost as much.

+1, You only straightened out the gross damage, now go to the bike shop
and have the hanger aligned properly..

Well, I imagine you being someone with over 11,000 post, you might know what your talking about. I guess the only thing to do now is have the LBS take a look at. I'll let you guys know how it works out.