I found the problem that Lithuanian accented letters are missing in map view (names of the cities), although they were displayed correctly in menu. I run simutrans on debian wheezy (simutrans version 111.2.2) with pak64, however I checked the newest stable 112.3 and the problem is still there. This is because a special symbol (paragraph sign) is missing in the start of the file as well as the file contains wrong letters. This might have happened while the file was converted to UTF-8. I attach my solution to the problem and hope it will be of use to others as well.
Thank you for notification.