If you see a watermark on compressed video, it could be for a couple of reasons.
The Stomp "demo" watermark looks like this (it's burnt into all encoded video when in demo mode):

If you see some other watermark, the chances are that you're seeing a watermark from some third party codec. A good example is the 3ivx codec, which places a huge red watermark over the entire video. If you see a watermark that's different to the one above then it pretty much guaranteed to be from some other source (aka: check your third party codecs).