I am currently trying to watermark a .FLV movie with and keep having trouble with gradients. The Watermark File is a TIFF and the image is on the Alpha Channel. The problem is that where the image should be clear it picks up a grey gradiant and there is also a outline around the watermark. I have run different number of tests on a number of different files and have still not come up with a solution. This last image is the closest i have been able to come to the desired result.
Did you try to modify 'Transparency' parameter (in Watermark Editor -> Filtes tab)? If it doesn't help, could you send us the TIFF logo? We'll examine it and see whether we can do something here.