Are you replacing the whole "framework-res.apk" file? If so then you will need to resign your entire ROM. Why? When you change a system file ("framework-res.apk", "com.htc.framework.apk", "twframework-res", "rosie.apk", etc.) it no longer has a matching "signature" for all the files it serves images to. Plug your phone into your computer and open up "ddms" in your android_sdk > tools folder to watch what happens when the phone boots up.
A workaround (The way I do it, it's more fun IMHO) is to open up your .apk files in 7zip (or if you're on a mac BetterZip) and add the images from the themed .apk to your stock .apk. This way makes it so your original .apk has the same signature as your other system files yet has the new images from the other files that you wanted. I've had a lot of luck with this method. I don't know if it will still work if you change any .xml files as I have not messed with those yet.
I've subscribed to this thread so if you have any questions post back here or you can PM me if you want. I'm on XDA all day, every day so I'll try to help as much as I can.
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