The S-Video circuit uses an AD724 to do all the RGB mixing trickery, so I'm not sure exactly what it does as far as filtering is concerned.
You could try a few things to find out where it's coming from:
1) Change text and background to pure blue and CLS. Then check pins 2,3,4,5,6,7,8 and 9 of IC115 (AMS48464). They should all be 0. If not, it's the ASIC that's generating the strange colour.
2) If all are 0 (as I suspect), then the problem is leakage between the analogue signals. The RGB outputs from IC115 are pins 15,16 and 17 - B, G and R. With no monitor connected and the CPC turned off, the resistance between 15 and 16 should be about 7.5K, the resistance between 16 and 17 should be about 7.2K and the resistance between 15 and 17 should be about 8.2K - Check if that is what you are getting.
If the values are lower, then you are getting signal leakage from one colour to the other.
Bryce.
Edit: good point TotO, if the cable is too long, you might be getting cross-talk in the cable.