I really don't know why this happens. My graphic card isn't the best but is that the reason that effects are "invisible" after a time?

When there are too many effects/units/whatevers on screen, effects start disappearing. It doesn't happen too much on stock maps for me, but on custom maps that have a lot going on (Bantha's maps come to mind) effects disappear all over the place. You might be able to lessen the number of disappearing effects by lowering your graphics settings.

Yes Banthas I know what you mean

I have the lowest settings.
I think i have to live with it.