Funny how something so small and really hard to see can cause so many problems with other programs! What I had a problem with is when I imported my uv'ed mesh into zbrush I would get strange red marks when using Uv check, this means the uv have have moved across eachother! The second image shows the cause of these, the 3 uv's that have just strayed across the mesh have caused all these problems! I have moved them back now and all is well!
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