Upper image saved from output node.
Lower saved from viever node
The problem is in sequence of 240 frames. Only images started from 125 to 160 have this issue - they darker.
If I rerender them one by one the bug continues.
If I use F3 key and save images from VIEWER node then it’s OK.
Wierd… Don’'t understand this issue.
Well, you are not saving alpha and z channels with file output, but they are connected to the viewer node. Any chance this is what is different? You have Normalize node as well so it’s like auto levels in Photoshop, might you have any objects that are close to camera but are not visible in the effected frames, so the minimum values change in z channel?
No bro, it does not matter what is output node connected with.
And to viewer node as well.
The problem appears at the middle of a SEQUENCE.
For example frame 124 is OK and 125…159 are DARKER. And 160 is OK again.
Blink!
No hidden objects etc nothing.
In a movie it looks like damn flickering.
I found that setting camera clipping (END) to 109 instead of 200 fixes this problem with brightness but cuts all my objects badly.
Now the only solution for me is RE-render all bad frames step by step and save them by F3 from viewer.
And if I use this way there is no difference between frames in that sequence.
Thank you.
Well, I managed to replicate the issue, I think, at least. I am not sure, but it seems to randomly decide to apply color management or not to. In my test cases it worked to add Curves or other color correction node that does nothing in between the normalize and output file nodes to force color transforms being applied, I am not sure how exactly this works, there might be a bug involved. You could try my solution see if the curves node helps in your case.
It does make sense not to apply color management for say normal pass or other passes, I wonder how Blender decides what is what with File Output node since there are no settings regardiong color management in it. I guess there might be an issue somewhere in that process. Does any of this theory make sense?
I located the problem but didn’t find solution yet.
May be I’ll create come kind of bounding box…
Found the solution.
Instead of using Normalize node I used Map Range node that allows me to set the limits according to Camera clipping range.
Well, at least you have something to work with now. I am sure you will find a solution(for example change Normalize node to something that will have fixed min and max values). You should still keep an eye on the color management issue. If you save with f3 with Save as Render checked (that should mean apply color management), with it unchecked(no color management), with File Output node with vector connected and with File output node with color connected, you can get 3 different results! 
It appears, Blender’s color management is messed up and it handles colors randomly everytime . It might not be an issue for you - I am using a monitor with a profile quite different from sRGB, so it might not be an issue at all with an unprofiled monitor that will be using sRGB in all cases a file is saved. Anyway, it’s good to be aware of Blender’s issues with color management. 
