Captain, at the moment there are no other such reports, perhaps there is a problem on your end, could you please try to reinstall the game one more time and perhaps reinstall Steam as well?
Regarding permanents upgrades - this is a feature at the moment, you can sell a ship with permanent upgrades to players but not npc
regarding image - it seems I got your message wrong, the warning is from ships->put on sale option
In case it is Captian Lord Tridax - he has been banned for 7 days due to multiply chat abuse reports. Once the duration of ban is completed, he will be able to use chat again. Any future discussions of this case (e.g. Captain wants to know the reasons) must be done here
At the moment there are two options:
1)Dismiss - a ship is gone forever;
2)Move to Docks - a ship is moved to your docks in a port
It might be improved within UI rework at the later stage
We do aware of this bug, Captain, thanks for the report
The current workaround for the cases with hidden items when you convert fish right before you enter a port is to relog, the rest of cases are under investigation
Check the download folder where you download files from internet, e.g. in case you use chrome press Ctrl+J, this program does not install itself on your PC