I am having this identical problem using my Quadro 4600's.
viztesting:~ # export DISPLAY=:0.0
viztesting:~ # nvidia-settings -q GPUCoreTemp
Attribute 'GPUCoreTemp' (viztesting:0.0): 56.
'GPUCoreTemp' is an integer attribute.
'GPUCoreTemp' is a read-only attribute.
'GPUCoreTemp' can use the following target types: X Screen, GPU.
In my '-q all' there are no other temperature identifiers, and in the GUI I am able to see both core temperatures. I have tried this both with and without the SLI bridge.
my nvidia-bug-report.log is gzipped at:
edit: Though the CPU's do say AMD Engineering Sample, these are just thermal test kits from AMD and have been proven to have full functionality.
edit #2: on line 1948 of the nv bug report... it begins to say that only 1 gpu would be used for this screen... this is only because I currently have the SLI bridge removed. Though, still in the gui, I am able to see the thermals of the second gpu.