it could be to do with the box command that used in matrix, this does not clear when cls it called works fine if you do this.
SYNC ON
SYNC RATE 60
RANDOMIZE TIMER()
DO
CLS
xPosition1 = RND(SCREEN WIDTH())
yPosition1 = RND(SCREEN HEIGHT())
xPosition2 = RND(SCREEN WIDTH())
yPosition2 = RND(SCREEN HEIGHT())
BOX xPosition1 - 20, yPosition1 - 20, xPosition1 + 20, yPosition1 + 20,rgb(255,255,255,255),rgb(255,255,255,255),rgb(255,255,255,255),rgb(255,255,255,255)
BOX xPosition2 - 20, yPosition2 - 20, xPosition2 + 20, yPosition2 + 20,rgb(255,255,255,255),rgb(255,255,255,255),rgb(255,255,255,255),rgb(255,255,255,255)
SYNC
wait 500
LOOP
Dark Physics makes any hot drink go cold.