Tony, it sounds like you are about a day ahead of me with the same problem.
I have been able to manipulate font size from the sliders in the "dimensions" section of the watermark dialogue box; "Width" and "Height".
But, it is not a consistent look if, especially if you have mixed your landscape and portrait images together and trying to batch print/ process them all at once.
I think I understand Kirk's explanation, but I am unclear why there is a "font panel" size option provided at all, (unless that is just a default font panel dialogue that was used and is auto overwritten)
The watermarking is a great feature and nicely keeps everything local within PM, but perhaps there is a 3rd-party program that can take the same info and image from PM and merge into one image file and that uses a rubberstamp as opposed to more flexible watermark process???