I'm actually not that surprised that you'd see signals of this sort. First, there's no real "source". Your scope's impedance is at least 1 MOhm, while the input impedance of your 6052E channel is 100 MOhm. Therefore, since there's very little resistance on the line, it's very susceptible to electrical noise.
Something you might try is looking at the diagrams on the BNC-2120 user's manual. For the FS mode (Floating Source), they suggest a 4.99K resistor from the negative side to the AI gnd. That way, you dissipate all that noise through the AI gnd. If the noise isn't attenuated a lot, it means that it can supply a sufficient amount of current, and will corrupt your real signal.
Mark