That's wacky. That second column is the number of hard links to that inode. Having over 65000 seems unlikely. I think you have some filesystem corruption.

Try booting into single-user mode (Cmd-S during boot) and running an fsck against your root partition. (Type "mount" in a terminal before you reboot to find out the device name. It'll look like /dev/disk0s2) In fact, I'm pretty sure you definitely need to do this. Your filesystem is almost certainly corrupt.

I'd also download SMART Utility (I'm pretty sure you can run it as a trial) or install smartmontools (MacPorts is probably the easiest method) and see if your hard drive is failing.