More testing, this is getting strange.
I took a lens-cap to cover VF, and it didn't change between AF/MF. Then I removed the lens cap, and still no change. And I'm sure it happened before.
So I turned my camera slightly to take different picture (with different exposure), and the problem came back. I put the lens cap back on VF, and still the problem stayed.
I changed different apertures (1.4....4.5), and the problem stayed. I turned the camera around for different directions, the problem stayed.
I took pictures with AF and MF (1/125 and 1/100), and the histograms for each were as expected, so MF 1/100 had more on the right.
The shutter speed indicator will jump the instant you flick the switch, you don't need to half-press the shutter. So take exposure with AF for 1/125, switch to MF and it changes immediately to 1/100, back to AF and it's 1/125, MF and it's 1/100.
And now no matter what I did, I cannot get it back to "no problem", which I got briefly few minutes ago.
Also no (bright) light shining at the top screen, and my model is anyway newer with the fix.