Alex,
I found a most common solution. I have slightly modified the powerdot.cls to suit my needs.
I'm surprised you didn't use my ready to go solution but spend time on modifying a class file. If you would have inserted \pdsetup{logopos=} in an ERT box in lyx, or else export the lyx file to latex and do it in the latex source, it would have saved you countless hours I guess... -Hendri.