Bleh, Spent the day hacking on Metacity. Seems that on a slow system the task of changing destkop takes so long to list all windows, stack them and get frames around them that it swallows keyboard input for a while.
The execute code waits for a return signal, less good on same systems. (it does some netcat magic to send signals to a jukebox.. However, why lock up the whole desktop while waiting for netcat to load?) . Solution is either to wrap the exec, or do something in the background.
Finally dealt with the "mouse move window" issues, ugly patch of a patch (limited resources patch in Fedora). However it worked , and windows no longer stick about.
Added some timestamping/debugging to metacity logging to try and deal with the lost keyboard issues. Economy still at the bottom, life sorta sucks.