Parts of the window do not get repainted

I have problem with part of the window which is occupied by panels that have a graphical content to display like graphs and strings. This content is created dynamically, it always changes depending on the values of different textfields, scrollbars, etc. For each graph (and I may have up to 5 of them visible) I have a class which extends JPanel with paintComponent() method displaying info needed for the graph, like tick values, and then in the middle of these panel I place another panel where actual graph is drawn (paintComponent() again). I have numerous problems with this part of the window, when it gets obscured by anything like other window, dialog, tooltip - in that case, nothing gets repainted automatically, rather the portion of the graph just dissappears, until I do some action which has an internal call to repaint(). The problem exists only for these panels, other parts of the window work fine.
Any ideas of why it might happen?

Is it just the one central panel that does this? If so you can load it into a test app and start tracking down the trouble. If it is more than one of the five panels... try making a test app you can show us.
I usually think of super.paintComponent(g) and the opacity property with this kind of trouble. Proper use of super.paintComponent will take care of the automatic repainting. If you setOpaque(false) then you'll have to handle the repainting yourself.
The other area to look through is your event handling, especially scheduling. And the possibility of the need to call revalidate or validate on your panel(s).

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