Check the noise relative to the specs of the scope, rather than between channels. If the noisier channel is out of spec, then there's a confirmed problem. Otherwise, your scope is in spec. I don't particularly see a reason for defining acceptable limits on noise equality between channels.
Having said all that, the channels are supposed to be identical circuitry so it is some sort of cause for concern. Although, at the same time, I'm always skeptical of these people who test the noise floor of their scopes by leaving the inputs unconnected. Unconnected means open circuit, high impedance, extreme noise sensitivity. It's entirely possible that the noisier channel just has a noise source physically closer to it on the PCB, but the problem goes away once a reasonably low-impedance signal is attached. Of course, 10x probes hardly affect the impedance of the node, but still. It'd make more sense to me to connect a terminator to the input to test noise floor, and would at least help with diagnosing your issue.