OK, just thought I would share this incase you run across it. Took me a little while to figure out so I thoguht I could save someone some frustration. I have only attempted to theme the stock deodexed ROM by Fabolous. It may be this way on others, dunno.
When you decompile the framework, I don't think something with our current tool set knows how to handle the new stuff so, it renames things it doesnt understand. THen when you recompile (and it will successfully) and install it completely messes stuff up. The issue I ran across was when theming the lockscreen images. While they are there in the drawable-xhpdi folder, they are not the ones you need. The ones you need are in a folder called drawable-xhdpi-v13. Problem is, that folder doesn't exist in the original uncompiled ROM. So, you have to rename it back to what it should be called which is drawable-sw600dp-hdpi.
Don't know if there are more but, just getting this out there for people trying to make themes.
Please feel free to share any other experiences or things you have learned in this thread about ICS quirks.