I know this is a dead thread, but the problem still persists (even with very popular themes) and I've found a more complete workaround...
Instead of just changing the file names to "@2x.png", if you also go in and scale the image up to 200% (using any image editing software) it will line up correctly and work as the theme intended.
So, the re-hash the whole process...
1: Using SSH, access the iPhone's root file structure.
2: Navigate to the directory for the image files you want to change.
*Slider - "/Library/Themes/[theme name].theme/Bundles/com.apple.TelephonyUI"
*Battery - ""/Library/Themes/[theme name].theme/Bundles/com.apple.springboard"
3: Add "@2x" to the end of every png file name before the ".png" extension (eg. "bottombarbkgndlock@2x.png")
4: Download all the renamed png files in the folder to your computer.
5: Using any image editor (photoshop, office photo manager, paint), scale the image up to 200% (both height and width, eg. 264x129 pixels becomes 528x258 pixels)
6: Transfer the altered png files back onto the iPhone, overwriting the original renamed files.
7: Ensure the theme is active in WinterBoard and respring or restart your iPhone.
I got this working in iOS 5.0.1 (redsn0w jailbreak)
I there's anything else that seems small or is not displaying correctly, what I did is download the whole .theme folder to my computer and searched for all png images within it. In a thumbnail view you should be able to find the file(s) that affect it and resize them accordingly. When done, you can just overwrite the whole .theme folder on the phone instead of overwriting the individual files one-by-one. Many files don't seem to require the "@2x" suffix, but you'll need to experiment if you're not getting the results you want. Good luck!