I have an article system that uses pop-up crosslinking successfully, but it is for a non vb related program. Would taking a look at the code for that help any? If so, I'd be more than happy to send it to you. I don't use the system for the fact that I prefer a more integrated article/glossary system than this one. But the code is very good. I can send you the relevant parts of code if you like.
Here it is in action:
http://onlinedebate.net/lore/article.php?id=004
There is a right margin, so decrease the window size of your browser until the horiz bar n the window appears, then adjust the window accordingly. What happens when the word is near the right side of the page, is that the pop-up re-adjusts its right edge to match that of the right edge of the window's display (so it never goes off page).
Don't know if it helps, if so, pm me for more info.