In MED and in Skin Editor theway of choosing a vertex is identical.

Only things I can think of:
- Look at 'File' --> 'Preferences' --> 'Misc' and increase the 'Vertex Size', it should be 3, at least.
- Look at 'File' --> 'Preferences' --> 'Video Out', and click the button under video out, to choose different render settings.
- Did you download the last version from the download site?

http://www.puppenheim.org/
http://www.wuerfels-welt.de
Old Game Tutorial: http://www.puppenheim.org/MITutorial.zip
Free Game Editor: http://puppenheim.org/AlienalsWeihnachtsmann.zip
http://www.puppenheim.org/blender_starting_main_settings.txt