Make sure your using uv1 for diffuse and only uv2 for your lightmap, the game doesnt seem to recognise the texture as a lightmap if its attached to uv3/4/5 etc.
I dont think there is a limit on the number of channels since ive seen units using uv1-uv6 in the stock files but as a lightmap channel you can only use uv2 for some reason.
As for youre issues with max i cant really help, i have max2010 but never really use it apart from for messing with materials on obj files made in maya.
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