It's also easier to evaluate if you shoot in RAW mode as well. That way the in-camera processing wont monkey with the sharpness and trick the brain into thinking something is sharp when it isnt. Also make sure IS is turned off because IS no matter how you have the camera mounted will shift the image possibly causing inconsistent image sharpness.
I just bought FoCal. It seems to get good results. Hopefully they will improve support for the 5D2 and 5D3. Manual mode is tolerable, but I sometimes felt like fidgeting with the controls and keyboard was undermining the delicate nature of the testing. A few times it told me the target had moved. Um, well... yes, because I'm hitting effing buttons during the test.
Try reading a book or watching TV while the Auto test is running. You might get better results.
That would be nice!
Alas... my 5Ds only work in manual mode. But still, I'll take it; it's a lot easier than the setup Neuro diagrammed.