I've stacked a ton of watermarked S2 clips since it came out. Tons of times I've uploaded the same clip twice in a row with it turned off, one had the watermark, the other doesn't. My best advice is to check right after you upload. It sucks but it saves having to do tricks over again.
edit: If anybody has watermarked clips that they don't want, I'm making a montage of watermarked clips, so feel free to send them my way.