I have also seen this. While the behavior and efficacy of dyes and quenchers are somewhat dependent on the neighboring nucleotides, its more likely that it the difference in fluorescence intensity is related to differences in batch-to-batch synthesis efficiencies. I've seen large differences in solution color at 100mM with identical sequences with identical dyes synthesized at different times. I'm guessing that a portion of the sequences synthesized are missing the dye and that this is accounting for differences in the color.