Ok so my original solution for this was to try and install clocks from this thread
http://forum.xda-developers.com/show...87&page=18#178 but none of them have worked. I think my problem may relate to changing themes over and over. (the clock changes work on theme changes)I went back to the original theme and magically had a transparent clock. Then somehow my phone got restarted and it went away. I'm really confused. Does anyone have any ideas?