Hi Andrey,
please post complete logs of a working and non-working probe as well as the exact flashrom version you are using. The output of lspci -nnv might become handy as well.
Thanks Stefan,
even giving out a fact that I am very lucky to hit very twisted issues at all, this time it looks like chip eventually stopped to respond via an appropriate interface (slight voltage change? bit-flip during a board initialization? lack of a probe delay? ), so I think that the initial report could be incorrect, as the flash is not responding anymore even where is was supposed to. Nevertheless, the appropriate log and lspci output are attached, please take a look on them if they could be helpful.