I first raised this as a side comment on ver 8.1 (I think!), when the change log gave no details on what was amended. I noticed that the time shown at the trading port differed from the one in effect at the military advisor. It wasn't just a rounding error (e.g. 3h1m Trading Port, vs. 3h18m actual journey time) and it continues to the present version. In that example, it was on a server with a shipping time bonus (Herakles .EN) and in a town with Sea Chart Archive, using Oligarchy and I wanted to know which "positive effect" wasn't being considered. I assumed that it was the Trading Port info that was/is faulty and so I didn't push the issue much.
Now, however, I've just bought a Freighter and sent it on a journey (Beta .EN). Trading port gave a time of 7h18s (not 18m), but the actual time shown at the military advisor is 1d16h (max level Sea Chart Archive, but Technocracy, so government is not impinging on the calculations). I really can't let this go unqueried, as it is so large that it would make future planning highly difficult. As noone else has raised this, I suspect it might not be a universal problem - can anybody replicate this?