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Just to close this out after Martin's and Adam's suggestions, I ended up trying another filter (Antila's ALP-T) and had the same result of patterned flats. It appears to be a common effect between the 294 sensor and light pollution filters.
However, I've since found out that this color pattern WAS actually appearing in the lights too, it simply only became visible though in a single sub if there was extra "light" in the sub e.g. passing cloud, approaching twilight or shooting towards the moon or in a brightly moonlit sky.
In short, it's calibrated out fine in the final image by using these odd flats.
Thanks all for the input.
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