I believe I understand what you're describing and it's been a long time since I've had this 'issue' but if I remember correctly, it's a function of your shell, which I believe is going to be bash. It tries to be intelligent about its symlink handling. It remembers the cd path you used to get to that symlink and 'cd ..' sends you back the same way you got in. It basically treats symlinks as real directories, not pointers. This can be very useful but it can also be annoying. I'll bet if you use tcsh, which uses a more literal interpretation of the file-structure, it would work as you expect. I wasn't ever interested in it enough to see if it could be disabled in bash.
I believe the proper option is -P as in "set -P" in bash to disable this feature (IMHO very useful).
Cheers, MaZe.