Several of us here have done parallel tests with different labs, and different results seem to be the way things go.
Two different labs can show different result because they use different lab equipment (the case between my GP and uro - completely different machine manufacturers), they use a different test, or they report results differently (my GP reports to three decimals, my uro tests to two, rounds down, and reports to one, so 0.499 at my GP is 0.4 at my uro). The key seems to be having the same lab do all of your tests, and always the same test (lets say standard or ultrasensitive as desired, but always the same), and last to understand how they report.
Everything in the test process which is not identical is different, and adds uncertainty.