This is happening to me on Hardy with 2.6.24-16 when copying large numbers of 
files.
  
  Weird thing is that Compiz remains perfectly responsive (desktop switching) 
but every other application including Firefox and and the terminal emulator 
continue to remain unresponsive for me minutes to *hours* after the disk I/O 
has finished (copying a few thousand files from USB to HDD using cp).
 
   This happens despite processor and RAM usage both staying under 40%.

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Heavy Disk I/O harms desktop responsiveness
https://bugs.launchpad.net/bugs/131094
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