Shell silently ignoring commands on certain files/directories

I an starting to see some wierd behavior, not sure if they are related. One of the issues I am seeing a lot is that software packages do not update well via their respective update feature, this includes even apple provided updates. Installing via a separately downloaded update packages works. I also today noticed that I was unable to install DoubleCommand, including the previously installed version. But this is more of a "freak" problem that I cannot put my finger on.
But what I can definately put my finger on is this "ignoring shell commands on certain files behavior".
For example I use the Saft Safari Input Plugin. After updating to the latest version I noticed that it wasnt working as an InputManager Plugin anymore. After some discussion with the author it became evident that the permissions are incorrect (directory is owned by "lsmith" and not by "root). Why this is even the way I do not know. Reverting to the previously installed version gave me the same behavior.
Pooteeweet:InputManagers lsmith$ ls -al
total 0
drwxr-xr-x 9 root admin 306 2 Feb 19:04 .
drwxrwxr-t+ 62 root admin 2108 22 Dez 18:17 ..
drwxr-xr-x 4 root admin 136 20 Dez 20:51 1PasswdIM
drwxr-xr-x 4 root admin 136 20 Dez 21:34 Inquisitor
drwxr-xr-x 4 root admin 136 13 Nov 23:37 PlaxoABAddIn
drwxr-xr-x 4 root admin 136 26 Sep 2007 SIMBL
drwxr-xr-x@ 5 lsmith admin 170 31 Jan 15:32 Saft
drwxr-xr-x 4 root admin 136 22 Dez 18:28 Smart Crash Reports
drwxr-xr-x 4 root admin 136 20 Dez 21:57 SpeedDownload Enhancer
Now trying to remove this directory from the shell has proven impossible. Eventhough I own the directory I cannot remove it. Not even via sudo. Same with trying to chown the directory:
Pooteeweet:InputManagers lsmith$ rm -rf Saft
Pooteeweet:InputManagers lsmith$ sudo rm -rf Saft
Pooteeweet:InputManagers lsmith$ chown -R root:lsmith Saft
Pooteeweet:InputManagers lsmith$ sudo chown -R root:lsmith Saft
Pooteeweet:InputManagers lsmith$ ls -al
total 0
drwxr-xr-x 9 root admin 306 2 Feb 19:04 .
drwxrwxr-t+ 62 root admin 2108 22 Dez 18:17 ..
drwxr-xr-x 4 root admin 136 20 Dez 20:51 1PasswdIM
drwxr-xr-x 4 root admin 136 20 Dez 21:34 Inquisitor
drwxr-xr-x 4 root admin 136 13 Nov 23:37 PlaxoABAddIn
drwxr-xr-x 4 root admin 136 26 Sep 2007 SIMBL
drwxr-xr-x@ 5 lsmith admin 170 31 Jan 15:32 Saft
drwxr-xr-x 4 root admin 136 22 Dez 18:28 Smart Crash Reports
drwxr-xr-x 4 root admin 136 20 Dez 21:57 SpeedDownload Enhancer
Now I am not sure what the @ in the permissions listing stands for, but I have similar issues with other files too. Note I am not getting an error, nothing. But also nothing changes.
Pooteeweet:temp lsmith$ rm sess_user1234
Pooteeweet:temp lsmith$ sudo rm sess_user1234
Pooteeweet:temp lsmith$ ls -al
total 16
drwxrwxr-x 4 lsmith admin 136 5 Feb 21:05 .
drwxr-xr-x 23 lsmith admin 782 21 Dez 21:55 ..
-rw-r--r-- 1 lsmith admin 0 5 Feb 21:05 foo
-rw------- 1 nobody admin 5286 4 Feb 17:23 sess_user1234

Thx .. the output is actually:
Pooteeweet:~ lsmith$ xattr -l /Library/InputManagers/Saft
com.apple.FinderInfo:
0000 00 00 00 00 00 00 00 00 04 00 00 00 00 00 00 00 ................
0010 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 ................
Also, I noted earlier that I am also seeing this behavior elsewhere in my XAMP temp dir:
Pooteeweet:~ lsmith$ xattr -l /Applications/XAMPP/xamppfiles/temp
Pooteeweet:~ lsmith$
So the issue does not seem to be a question of the additional attributes. Furthermore it used to work just fine installing Saft, and seems to work just fine for pretty much any other user. Moreover why can't I at least change the owner of the dir?

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