S-Video outputs on PC cards are generally pretty terrible and can cause exactly what you're describing. They work by basically attempting to take "anything" PC style and running it through a video masher until it's TV compatible. This generally means at least a scaler (resolution change) but also sometimes a framerate change since NTSC TV technically runs at 59.94Hz and not 60Hz (it's also interlaced while PC video is progressive). They don't usually do a very good job. The intent is to get "something usable" on the TV for things like presentations, not to provide perfect video. I would not be at all surprised if the S-Video output hardware on your PC's video card is causing this.
If you do want to use S-Video and ensure yourself full control over the video timings (necessary for "native" video output), what you seem to have to do is use the RGB output at native TV compatible timings (e.g. from an ArcadeVGA or using driver tricks like Soft15kHz on Windows to force this since no PC card will do this by default), and then use an outboard converter device like you can buy from arcademvs.com to convert to s-video. Note that there will be overscan. There's a thread somewhere discussing this at length. Results are generally very good (much better than the crappy onboard S-Video outputs), but it's complicated.