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The bar which contains the soft keys (home keys etc) used to be transparent, but now it has changed back to being black in colour after I tried a live wallpaper, even though I changed the wallpaper back and uninstalled the live wallpaper. Is there anyway of changing it back?
Sounds odd! Have you tried to restart the phone? Try to change theme in your phone.
Strange! Do you experience the same problem if you start your phone in safe mode?
http://talk.sonymobile.com/t5/FAQ/How-to-boot-your-phone-into-safe-mode/m-p/348008#U348008
You could also try to clear data for Xperia Home. Go to settings > apps > all > Xperia home > clear data. Restart the phone.