There are any number of reasons for occasional beachballs to appear. They will appear when some programs are involved in heavy disk I/O which tends to be processor dependent and causes the program to suspend all other activity until the disk activity has completed. This is more often the case when writing to the disk. Beachballs may also appear if the OS has to use disk I/O and is slowed down by an over-filled and/or fragmented hard drive. The fuller a drive gets the greater the likelihood that fragmentation will become a more noticeable problem. Beachballs can appear if you are low on physical memory so applications must resort to disk-based virtual memory which is considerably slower and tends to cause the computer to become slow or unresponsive for a period of time. It can also cause disk-thrashing. Beachballs can occur if the disk has become corrupted causing applications to have difficulty reading from or writing to the disk.
It is possible to repair a drive's directory, and it's even possible to identify corrupted files, but it's not possible to repair corrupted files nor repair a corrupted drive. If a drive develops corrupted files either the files will need to be replaced or deleted. If a drive develops soft sector errors these can be repaired by erasing the drive (reformatting.) If a drive develops hard sector errors these may or may not be repairable, but if they are repairable it requires zeroing the data during a disk formatting operation. If the disk directory becomes corrupted that can be repaired using Disk Utility or one of the various third-party utilities such as
Disk Warrior. Disk Utility can repair many but not all directory corruption problems. What DU cannot fix Disk Warrior usually can.
You can start repairing a drive as follows;
Repairing the Hard Drive and Permissions
Boot from your OS X Installer disc. After the installer loads select your language and click on the Continue button. When the menu bar appears select Disk Utility from the Installer menu (Utilities menu for Tiger and Leopard.) After DU loads select your hard drive entry (mfgr.'s ID and drive size) from the the left side list. In the DU status area you will see an entry for the S.M.A.R.T. status of the hard drive. If it does not say "Verified" then the hard drive is failing or failed. (SMART status is not reported on external Firewire or USB drives.) If the drive is "Verified" then select your OS X volume from the list on the left (sub-entry below the drive entry,) click on the First Aid tab, then click on the Repair Disk button. If DU reports any errors that have been fixed, then re-run Repair Disk until no errors are reported. If no errors are reported click on the Repair Permissions button. Wait until the operation completes, then quit DU and return to the installer. Now restart normally.
If DU reports errors it cannot fix, then you will need Disk Warrior and/or Tech Tool Pro to repair the drive. If you don't have either of them or if neither of them can fix the drive, then you will need to reformat the drive and reinstall OS X.
This applies to your startup volume. No need to repair permissions on any but a startup volume.
