I’ve found the select by polygon functionality doesn’t seem to work properly, at least with point shapefiles. If you try and use it on one of these it may select the correct nodes the first time, but generally if you then do another selection it doesn’t work - either selecting not enough points, too many points, or points nowhere near the actual selection. I am using MapWinGIS 4.9. I’ve also confirmed it doesn’t work properly in MapWindow 5 either, so it’s not my code.
Addendum: It seems the more points you add in the selection, possibly with shorter distances between them, the better it works.