Yah... I've come back to the conclusion that the core link (and fileticket) module is broken, this may or may not be your site's problem as well. 

For our site we see the same behaviour (broken links, etc) in the link module as well as in FCK. I've done more testing, but since there's no documentation on linkclick or what a fileticket is, there's no hope of decyphering the problem without hours of wading through the code, so I'm giving up on it for this site.  I've posted some queries over on the Link module's forum, but have gotten no answer's there.

Maybe they've fixed it in the current version... but, since we're about to launch, I'm not going to even try to upgrade.  For now, I've warned my content editors not to use the "server browse" feature of the editor and to just hand code relative URL links (e.g. "/portal/0/docs/my.doc") using the other: protocol in the link dialog box.  You should try this too, it's a bit of a pain, but it works like a champ (think of it as "old school" ;-).  Just means that your content editors need to know where the files are in your site's document tree (maybe have the file manager open in one tab/window and the content editor in another).

Take care,

GregC