The Knytt Stories Manager (the only third party tool) won't work if the path leading to its directory is too long. Try moving your Knytt Stories folder to the top of your C drive (or whatever drive you want the game on).
Also, in before relentless plugging of the
function combined with needless use of its icon to "look cool."
If this doesn't work, please specify what the error message says.
edit: reduced ambiguity