This has to do with ATI + lua point drawing :
http://springrts.com/phpbb/viewtopic.php?f=11&t=24036
Bug is not solved. Every lua using GL_POINTS will make the big points appear.
To avoid it in smoothscroll, you can edit the widget and remove the lines that draw GL_POINTS. Widget will continue working with the line only.
If you use a non default UI (LUA), you can't deal with the minimap point drawing AFAIK. Only "solution" is to disable LUA map drawing (red UI / Ice UI / ...) and get back the stock minimap.
Personaly, I bought back an NVidia.