What code are you trying?
I have MaxGUI and this works for me in 'non-GUI' mode :
Strict
Local n:Int=0
Graphics 800,600,32
While Not KeyHit(KEY_ESCAPE)
Cls
SetPointer n
Flip
If MouseHit(1) n:+1
Wend
Can't you use the source to see how its done and then set-up your own?