Window flashing case 2
A program is not responding to anything after having mapped (made visible) a window under Ion. Either graphics are also not updated on the window or they're flashing rapidly.
The program may be fighting with Ion over window size. The ICCCM says:
The response of the client to being resized should be to accept the size it has been given [by the window manager, if any] and to do its best with it. Clients must not respond to being resized by attempting to resize themselves to a better size. If the size is impossible to work with, clients are free to request to change to the Iconic state.
Thus, if this fight is the source of trouble, the program is not conforming to the ICCCM. It is therefore seriously broken and should be fixed.
See also: Window flashing case 1.