Here's what the manual says:
"EV Compensation for M (Hyper-manual) and X (Flash X-sync speed)
For example, if the EV compensation value is set to +1.5 for M and X, an underexposure of 1.5 EV is displayed on the EV bar. if you set the exposure value so that the l is displayed at the center of the EV bar, the image will be captured with the compensated value."
This would fit in to the "Instruction manual typos" from a few months ago. Makes no sense, and explains nothing. I have shot about 3 images on M, so I don't really care about the function...:-) Oh, it also says no EV in Green mode.
I just checked it. Meter something at 0 EV, then dial in your EV compensation (the bar changes). Then adjust S or A settings to bring the bar back to 0 (center). The camera does not change S, A or ISO.
Seems rather pointless to have to use a bar to count f stops.
Should say:
"For example, if the EV compensation value is set to +1.5 for M and X, an >>over<<exposure of 1.5 EV is displayed on the EV bar. If you now >>change A or S or both to set the exposure<<< so that the l is displayed at the center of the EV bar, the image will be captured with the compensated value."