Hi,
i use it with Win10 without problems. This missing connection normally only appears, if the wrong board part is included.
Can you send me the whole log file, if you run vivado_create_project_guimode.sh?
Location: Starterkit\v_log\vivado.log
Which Linux did you use?
Which Reference Design Version? TE0803-Starterkit_noprebuilt-vivado_2018.2-build_02_20180723204638.zip or TE0803-Starterkit-vivado_2018.2-build_02_20180723204618.zip or older one?
br
John