Macs store some low level information in permanent internal memory called "parameter RAM" (PRAM). Different things are stored here depending on your machine - newer machines tend to store more. If this information gets damaged your machine might behave strangely and booting from a CD won't help because the information is in memory, not disk.
To reset Parameter RAM settings hold down the command option P R keys while starting the computer. The machine will restart, you should hear the startup chime twice, then you can release the keys. This will often fix various "unexplained" bugs.
Note that some functions, such as mouse speed, clock, and network ports might also be reset, depending on your hardware and OS.
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