Are you using a CFG file local to the project e.g. was the CFG file updated for CADWorx 2010 contents? I've had a couple of older projects do odd things with isometrics when an older CFG was being used, I think it may have been a DatabaseCodesISOGEN issue. Either way, using a current (and properly set up) CFG file resulted in proper isometrics.
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If you are going to fly by the seat of your pants, expect friction burns.