for the watermark to work in compressor it has to have an alpha channel.
when i was working on a show where we didnt have Photshop, i made the watermarks in FCP, using the simple text generator.
then exported using Quicktime Conversion to Still Image: TIFF format.
to add the watermark in Compressor,
go to the Filters pane in the Inspector, and tick "Watermark"
then navigate to your file, and adjust the settings to taste.
nick