Ubuntu defaults to the "Anticipatory" IO scheduler on boot up, when there is heavy disk IO by processes or applications running in background this can cause response issues that can be allievated by changing to "Completely Fair Queuing" IO.
I have taken these instructions (and take no credit for them!) from the thread at:
To have the scheduler set to cfq on boot, pass elevator=cfq to the kernel.
You can edit /boot/grub/menu.lst and add it to the kernel line for your current kernel, and add it to the end of the #nonaltoptions line to have it automatically applied to future installed kernels (do not remove the # at the beginning of the line!).
For some related documentation for those who are curious about the difference between the "Completely Fair Queuing" or "Anticipatory" IO schedulers: