Sounds like your PWD is inside a symlink.
will print the results from the parent directory of the target of the symlink
will print the results from the parent directory of the symlink itself.
For example, take the following
Code:
$ mkdir -p dir1/dir2/dir3/dir4
$ cd dir1/dir2/dir3/dir4
$ ln -s ../../../dir2/ dir5
$ cd dir5
$ pwd
/home/user/dir1/dir2/dir3/dir4/dir5
$ ls -l ..
total 4
drwxrwxr-x 3 user user 4096 2013-05-07 17:19 dir2
$ cd ..; pwd; ls -l
/home/user/dir1/dir2/dir3/dir4
total 0
lrwxrwxrwx 1 user user 14 2013-05-07 17:20 dir5 -> ../../../dir2/
$
The contents of "ls -l .." is dir2, the contents of "cd ..; ls -l" is the dir5 symlink. Just a difference in how ls and cd handle ".." from inside a symlink.
Of course this begs the question, "why do cd and ls treat ".." differently when inside a symlink?" Which then begs the more philosophical question, "what
is ".." when you're inside a symlink"?