It really strikes me as two issues, because I can't for the life of me figure out how the frequency would be effected by the level with this kind of generation - maybe there's something strange about the LO board or the lower band board that I just haven't dug into, but I can't think of something. If, for example, you had an LO underpowered that was feeding a mixer, you just would get varying/low power output at the expected frequency, not strange frequency variation. It's worth finding out, though, whether this frequency offset is repeatable or is linked to the frequency of interest or is just a fixed offset. That could point to a number of potential things, but if, for example, it was a specific LO that was under frequency for whatever reason, when you turn on a path with a doubling, you'd expect to see its offset double as well. If the variation is more random, then maybe it's from a VCO fault of some sort (though you'd think you'd see PLL errors with that), but I don't know of what could give you a wrong frequency offset in just one case. Is a modulation enabled and the modulation data just garbage?
For the level, yes, it definitely could be a switch. It would be worth just disconnecting the coax from the main synthesizer board that goes into the RF module with the switches on the 6GHz extension to measure to see if it's actually a fault in the output of the lower band board (though if the detector isn't seeing it and giving you an unlevel error, it's less likely). If not that, then I'd also check the drive voltages for the switches - just trying to eliminate the much easier to fix/replace options than trying to find new dies or a whole new 6GHz output module...