In either Simple or Full Desktop Mode, I found the keyboard frequently stopped working in a given application window (for example, my editor jEdit, or Konsole). The window would still receive mouse input, and key combinations received by the window manager would still work (e.g. Alt+F4 to close window) just not keyboard input to the application itself.
I eventually figured out that this happened when various keyboard shortcuts involving (for example) Ctrl+Shift combinations were used.
The solution was to disable the SCIM input method manager - I used the package-removal method described here, then restart the EEE PC. It has not happened again since I did this.
If you actually need SCIM, however, I don't know what the solution is!
As for me, I have the same symptoms for the mouse (not the keyboard). Happens mostly with kmail, but also with firefox. I do not have package scim installed though (dixit synaptic).
No idea how to fix it.