If you are truly in Manual mode (i.e. no auto-iso) and not using flash, then the exposure compensation setting should have
no effect on the resulting image. In other words, if you have two images with the same shutter, aperture, and ISO in the metadata,
then they should look like identical exposures regardless of how the EC is set. However, setting EC WILL affect the metering readout
in Manual mode. For example, let's say you determine your manual exposure settings by spot metering a gray card and zeroing the meter.
That will work fine as long as the EC is set to 0. If you change the EC, it will bias the meter readout by that amount. In effect, the EC in
manual mode changes the meaning of 0 with respect to the metering readout. For example, if you set the EC to +1 and then spot meter
a gray card and zero the meter, the settings you end up with will be one stop brighter than they would be if EC was set to 0. To get the
correct exposure with EC set to +1, you would spot meter the gray card and change the settings until your meter readout is at -1.
This is true for Nikon but not Canon. In fact, with Canon, there is no way to even enter an explicit EC in Manual mode.
But if you are using Nikon flash (prior to the D4), setting EC WILL affect the flash output even if you are in Manual exposure mode.
For example, setting EC to +1 in manual exposure mode will have no effect on the ambient exposure but it will increase the flash
output by one stop. The D4 is the first Nikon body where you can separate the ambient EC from the flash EC, making it work the
same way as the Canon system. More info here :
http://www.nikonusa.com/Learn-And-Ex...th-the-D4.html
The only explanation I can think of for what you describe where two images with the same exposure settings in the metadata look like
different exposures would be if the amount of ambient light changed between the two shots.