Hmm...

I've just re-read your first post.

If the shortcut is in the root of this directory so that the structure is:
Code:

-ROOT               [contains myshortcut.lnk]
    |
    |--BIN          [contains Kix32.exe]
    |
    |--SCRIPTS      [contains myscript.exe]


The the shortcut should be either:
Code:
BIN\kix32.exe SCRIPTS\myscript.kix


Or, if you must force a relative path:
Code:
.\BIN\kix32.exe .\SCRIPTS\myscript.kix


You shouldn't be referring to a parent directory at any point.