There's no time factor in MPG, only miles and gallons. You need to aim for equal speed so the aerodynamic load is equalized. Otherwise the skirted run might be faster, but has a quadratically higher drag load.
I'm puzzled by the result. Can you do a coast-down to verify the drag difference? It won't give hard MPG numbers, but it will show if the problem is in the test or in the mod itself.
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11-mile commute: 100 mpg - - - Tank: 90.2 mpg / 1191 miles
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