When I was playing around with the comparator, I tried to give the input directly with redstone and directly with repeaters.

When the Comparator is toggled and the signal strength is the same at input B and A, the following happens:

If you give the input over redstone, the output is as expected: As the inputs are equally strong, the output equals input A.

But if you give the inputs over repeaters, it's like B would be stronger than A, because the output is 0.

So my assumption would be that, when there's is a repeater directly at input B, B is always considered stronger than A.