It seems that there is a small bug introduced in latest (5.3.3.20820) version of NAPS2 which causes in batch (ADF) scan every second page to be 180 degree rotated. Please, see attachement.
I have scanned exactly the same document using my scanner's (OKI MC 342) default scanning software (OKI ActKey) and found no such effects. This seems to be rulling out the idea that this problem comes out of my scanning driver.
I have scanned exactly the same idea using NAPS2 3.0b Standalone (3.0.1.32217) and -- again -- found no traces of this problem. This seems to be confirming that this problem appeared on latest or one of the last releases of NAPS2.
I don't exactly recall when did I updated NAPS2 for the last time, but I'm pretty sure that mentioned problem appearead around beginning of this year and I had no such problems running older version of NAPS2 around October-December 2016.
If there is anything else I can provide to try to find source for this bug then just let me know.
It is hard to belive it (?), but after rising this ticket everything is now OK.
Then only thing I can think about (except ghosts or the fact that I'm going mad) is that this single run of NAPS2 3.0 Standalone cleaned some settings that are shared with NAPS 5.3.3. Is this possible at all?
I have also found an option "Flip duplexed pages". Going to test it along with your suggestions, once this weird case returns. But, for now -- this ticket can be closed.