I have now done enough testing, developing my own using Tetenal's E-6 kit and using two commercial lab's (sad that there are only two professional lab in my country).
It seems that big part was really on the lab side. So problem wasn't directly caused by flashes, but flashes bring it more visible due the underexposed backgrounds.


Next... I will use additional flash when ever possible and I have to calibrate my home E-6 kit's time...