I've been having the same problem.....I dont know of anyway you can automate except by using the matrix to set controls to the mod wheel. Then use the mod wheel control in the clip to automate. I know it kind sucks and is limiting your possibilities....but it works!
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TI Desktop - APC40 - MPC 1000 w/jjos - Poineer 800 - Best laptop IBM made in 2003 (~_~) - 2 Techs/cause real DJ's Play Vinyl and real producers should know how to at least 
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