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Sorry I should have updated this post sooner - I seem to have resolved the Chrome issue - I needed to save my comparison image as PNG rather than JPG. I'm no graphics expert, but seemingly something in how JPG's are encoded and PNG differs - I was capturing the JPG from IE, which resulted in a match, but something in how the two browsers render things is subtly different, but PNG somehow "resolves" this.
Don't ask me why, but touch wood it seems to work!
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Might be related to png being a lossless format? Just one idea as far as that part of it.