Hi Mike,
Are Universe 1 & 2 coming out of DMX Outputs directly on Ion?
How are those cables ran to the lights? Via a DMX Splitter? Length of DMX?
DMX cables and networking cables could have different results on output time. But it still shoudn't be noticeable.
You could check to make sure DMX Speed is set to Max.
In Ion->Shell->Setup->Local IO-> DMX Port - what speed is set there? Maximum?
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