I'm really starting to suspect hardware as well based on your comments here and elsewhere compared to others experiences. Or something really odd that you are doing based on your symbolic links comment.

I do remember getting really strange issues with my old Powerbook when the IDE controller was going out. It was very hard to detect, and a replacement mainboard fixed it. Initially, under certain load, the drive would get remounted read only due to errors detected. The hard drive was replaced, and the system was checked for errors for a while and came up clean. I took the system back, and began having similar issues again.

In the end, the combination of trying to install World of Warcraft off disc, along with being plugged in, and energy saver set to highest performance would reproduce the problem every time. Nothing else, including diagnostic programs found a problem. Something about the high CPU usage along with heavy IO induced the issue. WoW install discs use quite a bit of compression, so the CPU was busy during install.

It's possible your problems started with Leopard doe to a similar issue. Leopard does generally use more CPU time then Tiger with the additional thing added into the OS, and maybe it was enough to trigger the problem.

For the record, this is ny /bin on a 10.5.4 install on an Intel mac:
Code:
-r-xr-xr-x   1 root  wheel    46720 Nov 28  2007 [
-rwxr-xr-x   1 root  wheel  1244928 Mar  4  2008 bash
-r-xr-xr-x   1 root  wheel    43296 Mar  5  2008 cat
-r-xr-xr-x   1 root  wheel    56720 Apr 20 13:32 chmod
-r-xr-xr-x   1 root  wheel    56208 Apr 20 13:32 cp
-rwxr-xr-x   1 root  wheel   610864 Sep 23  2007 csh
-r-xr-xr-x   1 root  wheel    56096 Nov 28  2007 date
-r-xr-xr-x   1 root  wheel    59776 Apr 20 13:32 dd
-r-xr-xr-x   1 root  wheel    51424 Apr 20 13:32 df
-r-xr-xr-x   1 root  wheel    38336 Nov 28  2007 domainname
-r-xr-xr-x   1 root  wheel    38320 Nov 28  2007 echo
-r-xr-xr-x   1 root  wheel   114000 Mar  5  2008 ed
-r-xr-xr-x   1 root  wheel    46944 Nov 28  2007 expr
-r-xr-xr-x   1 root  wheel    38416 Nov 28  2007 hostname
-r-xr-xr-x   1 root  wheel    38640 Nov 28  2007 kill
-r-xr-xr-x   1 root  wheel  2103664 Sep 24  2007 ksh
-rwxr-xr-x   1 root  wheel   133312 Apr  3 19:48 launchctl
-r-xr-xr-x   1 root  wheel    38752 Apr 20 13:33 link
-r-xr-xr-x   1 root  wheel    38752 Apr 20 13:33 ln
-r-xr-xr-x   1 root  wheel    73696 Apr 20 13:33 ls
-r-xr-xr-x   1 root  wheel    38640 Apr 20 13:33 mkdir
-r-xr-xr-x   1 root  wheel    47696 Apr 20 13:33 mv
-r-xr-xr-x   1 root  wheel   218640 Apr 20 13:33 pax
-rwsr-xr-x   1 root  wheel    85536 Mar  4  2008 ps
-r-xr-xr-x   1 root  wheel    38400 Nov 28  2007 pwd
-r-sr-xr-x   1 root  wheel    56208 Nov 28  2007 rcp
-r-xr-xr-x   1 root  wheel    47616 Apr 20 13:34 rm
-r-xr-xr-x   1 root  wheel    38352 Apr 20 13:34 rmdir
-r-xr-xr-x   1 root  wheel  1244960 Mar  4  2008 sh
-r-xr-xr-x   1 root  wheel    38464 Nov 28  2007 sleep
-r-xr-xr-x   1 root  wheel    55744 Sep 23  2007 stty
-r-xr-xr-x   1 root  wheel    38128 Dec 10  2007 sync
-rwxr-xr-x   1 root  wheel   610864 Sep 23  2007 tcsh
-r-xr-xr-x   1 root  wheel    46720 Nov 28  2007 test
-r-xr-xr-x   1 root  wheel    47616 Apr 20 13:34 unlink
-rwxr-xr-x   1 root  wheel    38544 Nov 20  2007 wait4path
-rwxr-xr-x   1 root  wheel   982000 Sep 23  2007 zsh
-rwxr-xr-x   1 root  wheel   982000 Sep 23  2007 zsh-4.3.4