What appears to be happening is that the command line version is failing to compile with the following error:
build/server/gui/components/gui_image_list.o: In function `gui_image_list_t::draw(scr_coord)':
gui_image_list.cc:(.text+0x317): undefined reference to `display_veh_form_wh_clip_rgb(short, short, short, unsigned short, bool, unsigned char, unsigned char, bool, signed char)'
gui_image_list.cc:(.text+0x5d0): undefined reference to `display_veh_form_wh_clip_rgb(short, short, short, unsigned short, bool, unsigned char, unsigned char, bool, signed char)'
build/server/gui/convoi_detail_t.o: In function `gui_convoy_formaion_t::draw(scr_coord)':
convoi_detail_t.cc:(.text+0x6d7): undefined reference to `display_veh_form_wh_clip_rgb(short, short, short, unsigned short, bool, unsigned char, unsigned char, bool, signed char)'
convoi_detail_t.cc:(.text+0x749): undefined reference to `display_veh_form_wh_clip_rgb(short, short, short, unsigned short, bool, unsigned char, unsigned char, bool, signed char)'
build/server/gui/convoi_detail_t.o: In function `gui_convoy_maintenance_info_t::draw(scr_coord)':
convoi_detail_t.cc:(.text+0xfdb): undefined reference to `display_veh_form_wh_clip_rgb(short, short, short, unsigned short, bool, unsigned char, unsigned char, bool, signed char)'
build/server/gui/convoi_detail_t.o:convoi_detail_t.cc:(.text+0x1078): more undefined references to `display_veh_form_wh_clip_rgb(short, short, short, unsigned short, bool, unsigned char, unsigned char, bool, signed char)' follow
collect2: error: ld returned 1 exit status
common.mk:21: recipe for target 'build/server/simutrans-extended' failed
make: *** [build/server/simutrans-extended] Error 1
This means that the old version of the server is running, which is incompatible with the latest pakset version. I am looking into this now.