I have the same problem on a fully updated Jaunty (amd64). After compiling a 
document a couple of times and editing in between, the editor does not accept 
keyboard input any more. Mouse still works.
Interesting: The keyboard shortcuts to access the menu Alt + something also 
work. And if I click in "structure" on "LABELS", the editor suddenly accepts 
input again. If I click on the editor window, then, the problem is there again. 
So this might have to do something with the focus?
The problem with headers not appearing, TerpInHotLanta mentioned, does not 
apply for me.

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texmaker stops responding to keyboard after saving
https://bugs.launchpad.net/bugs/348028
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