Regarding a voltage underrun, the VRMs on Cube Cards are actually fairly clever. There are two VRMs per card, each sourcing voltage to 8 chips. The regulator uses three resistors and a FET to select the high and low voltages. In one configuration, all three resistors are in the series divider for feedback sampling; in high-speed configuration, the FET shorts around one resistor which changes the division ratio for the sampled output voltage and shifts it up from 1.05V to 1.15V
(More information on Cube VRMs here http://www.gekkoscience.com/webuilds/cube_oc/cube_oc.html

What I would recommend is, with the card running, measure the outputs from the VRMs (across C99-103 and across C83-87) and make sure you have about 1.05V; then switch it to high clock and see if both VRMs changed to 1.15V

If one is still reading 1.05V, measure the voltage present on R25 and R26 and see what they read. If they're both reading about the same (several volts), I'd say the FET itself is bad or not properly connected. First I'd resolder the FET (Q3/Q4) and see if that fixed it.
If one is several volts and one is low, you're not getting the signal to turn on the FET and switch the VRM to high-voltage mode. I'm not sure offhand which logic driver controls this signal but it shouldn't be too hard to trace. In the case of no signal or a bad FET, a workaround should be to remove the R9 or R18 resistor (on mine, it was 1800ohm but I've seen some that had 2100 there) and short across its pads. This would force the VRM to run in high-power mode all the time, so it would be providing more power than is required for "low clock" but would be right for "high clock".