If nothing was wrong with the settings then the message wouldn't come up. That means something was messed up with the settings. That means LFS somehow confused itself. That means there is a bug somewhere (unless everyone with that message hex-edited his settings, which is unlikely, as I can confirm that the message comes up without any editing from my side).
Problem is that the bug is hard to track down, because I never noticed any impact of the game from that error-message. I can't figure out what LFS had a problem with. I speculate that there may be something wrong with the code that generates that message.
Perhaps it would help if Scawen improved the error message and for example added a more detailed line to LFS's logfile so we can see what was wrong.
Vain