Could you post an example?
It sounds like you have repeated measures of each of the 6 runs?
Unless you want to analyze the data using a mixed model in JMP Pro, a good alternative is to use the mean of the repeated measures and the log-transformed standard deviation as Y's.
The mean of the replicates takes advantage of the central limits theorem to give you a better estimate from a noisy system, and the Stddev lets you see if there is a portion of the design space that has less noise.
JMP Systems Engineer, Health and Life Sciences (Pharma)