I probably do not understand the question. But of course the windows disappear after minimizing. It is the goal of minimize button. The window should be now among tasks on the shelf
Lets try to understand again:
1. Does the window disappear when press the minim button?
2. Does the window disappear when double click on the window border?
3a. Do you see the window minimized on the shelf or no?
3b. If not, do you have task module loaded in the module settings?
3c. If yes, do you have the task widget placed on the shelf?
4. Aren't you switched to another desktop? Try ALT F1 vs ALT F2 or with mouse on the pager widget on the shelf
You have to give us more info Bolla to understand your issue. And yes, I agree with cordx. A screenshot should be fine to see...
Stefan