Some times before I shoot in low light situation, I put my camera in auto to see the settings to use as a baseline and tweak the setting from there. However, oftentimes, I am forced to use the auto because I would have to use to slow of a shutter speed or a high noisy ISO. My question is why can't I replicate the results when I use the same exposure setting in manual that showed correct exposure in automatic. See sample. First shot in manual and second in auto. Both shots were exposed at F4, Shutter speed 60, ISO 400 with automatic flash. What am I doing wrong? Please help.
Look in your images EXIF data to make sure the ISO was 400 in both when they were exposed. It doesn't look like it was. EXIF shows the settings actually used.
Auto mode uses Auto ISO, Auto White Balance, and it controls color profile too. Auto mode is Auto everything. But you don't set ISO to anything in Auto, Auto does what it wants to do. Your ISO setting might say 400, but Auto does what it wants. EXIF will show that.
In contrast, A,S,P,M are just exposure modes.
These modes do not use Auto ISO or Auto WB unless you configure them individually to be on. Default is off. You set color profile yourself too. And you turn the flash on if you want flash to be used.
Instead of using Auto mode for these comparisons, use Aperture mode A. A,S,P are auto Exposure, but then Auto ISO and Auto WB will be same as Manual, only on if you have selected them On. Auto ISO and Auto WB can have effect if they are on. But only Exposure should vary in A and M mode, and Manual can duplicate what A mode does.
But Auto mode is a whole different game, fully automatic, no manual control.
Depending upon what specific camera you are using, what settings you have selected, and in what particular "Auto" mode you are shooting the camera may change what you think is selected to make sure the image is properly exposed. Even though you think you have the camera set to ISO 400, if the camera decides it needs a higher ISO it can raise the ISO if you are in an "Auto" exposure mode that enables Auto ISO by default or if you have enable Auto ISO yourself.
The way the flash behaves can also vary between full "Auto" modes and Manual Exposure mode with the flash set to "Auto." If you are in Manual exposure mode and have some flash exposure compensation dialed in the flash will underexpose by the amount you have entered. If you set the camera to a full "Auto" exposure mode, the flash exposure compensation you have entered will likely be ignored.
If you would provide us with the specific camera model, specific lens model, specific flash model, specific "Auto" exposure mode, and specific flash settings used when in "auto" mode as well as when in Manual exposure mode it would allow us to give a more complete and specific answer.