The available memory calculation is an estimate at best and should never be used as the last word on how much memory is actually allocated or in use.
There have been cases where an Extension conflict or corruption have caused the memory shown to be less than is actually installed. Booting with Extensions off should be the first step in this process. If the memory allocation is correct you should then verify compatibility with any Extension installed.
If that does not resolve the issue, try these steps:
- Reset PRAM by holding down the Command/Option/P/R keys at startup
- Update the driver on the hard drive
- Do a clean reinstallation of system software