It's probably a security mechanism so that forum users can't embed nasty javascript code on the page. I would do the same if I were writing a forum product to be used on the internet. Javascript "viruses" can be just as nasty as the current crop of virii floating through people's email boxes.
Puppy, those kind of javascript URL's will never load when they open in a new page. Never Ever!
The only way to let ppl open them (since UBBCode automatically opens a new page) is to leave instructions for them to *right click* and *copy shortcut* into the address line of a new browser.
*Edit - I know this coz I have 2 boards of my own and one uses BBcode. So one will open javascript links on the existing page and the other wont.