Transport fluctuations and variations in a series of metal-molecule-metal junctions were quantified through measurements of their thermopower. Thiol bound aromatic molecules of various lengths and degrees of freedom were chosen to understand the magnitude and origins of the variations. Junction thermopower was determined by measuring the voltage difference across molecules trapped between two gold contacts held at different temperatures. While any given measurement was remarkably stable, the breadth of distributions from repeated measurements implies variations in the offset of the highest occupied molecular orbital (HOMO) relative to the Fermi Energy of the contacts, similar in magnitude to the nominal offset itself. Statistical analysis of data shows that these variations are born at the junction formation, increase with molecular length, and are dominated by variations in contact geometry and orbital hybridization, as well as intermolecular interactions.