I think I found a cause for this.
data/scripts/menu/Page Ships Journal.py
There's a fragment:
After deleting the line in bold, when I add new journal entry it appears with correct time. I'm not familiar with Python but it seems to add time zone modifier to already correct time, which would give effect I observed (entry time being off by hour difference between nautical and GMT time).
This is in TWoS 2.2.10.