Probably too late to get into this discussion (a month too late it seems), but here goes anyway...a safe boot is when you restart the computer but hold down the Shift key. This disables a lot of extensions and other things, in effect making the computer as "pure" as it can be; note, however, that due to this disabling, it also means you won't be able to do a lot of things you normally could. Safe booting is usually used as a method to see if the problem is in the computer itself or an extraneous error.

To repair permissions, open up Disk Utility (it's in the Utilities folder, under Applications), choose your hard drive, click the First Aid tab, and then click "Repair Disk Permissions".