I'm not sure I'm quite ready to say that there are no hardware problem, but it could be a software issue.
One of the thing you could try is to boot on the recovery partition and recover your OS. Prior to do this, you should make a copy of your HDD on a secondary drive. I don't mean a copy paste of windows, I really mean a duplicate drive. I did it using UBCD, it's quite easy and is definitely worth it (be careful not to wipe the scope HDD)! Of course test your duplicate. Then just boot on the recovery and try to run the cal in recovery, it might work. If not, recover the primary partition. If this doesn't work, reinstall the scope software, I doubt that it will work, but it's simple enough that it's worth trying.
You only have the Probe board that fail at the moment, I'm a bit surprised, I would have expected something closer to the ADC. I think you should follow the troubleshooting procedure in the service manual to find the issue.? It could very well be a unconnected cable. When I received mine, I had a similar issue (I had traces on all channels) and the issue was a connector plugged at the wrong place.?
I would be curious on seeing what the wave looks on the defective channel. Is it that the ADC is saturated, is it that the display overlay shoots nothing or something else. What happens when you try to measure something on that waveform? On other waveform?
