The Mms.apk needs to be named with a capital M. Otherwise 2 will exist. And the system will use Mms.apk instead of mms.apk. Try that, if it still doesn't work there may be a problem with it.
I would take an Mms.apk from another rom that uses dark background. I have been using a CyanogenMod Mms.apk since i got my blade. Always preferred the black background.
I use the CM mms too, I much prefer the dark as well.
Another thing you may want to check is that you're using the apktool 1.3.1 linked in Frankish's first post and not 1.3.2 which has "faults".