It was easier for me to write this out as a little tutorial to show you how it should work:
http://flatpress.georgi.co.uk/?x=entry:entry130209-072820
If it still doesn't work for you then maybe you could post a link so we can see what's going on in your case.
Yes, if you use my alternative BB Code plugin which adds this functionality. (I'm not sure if that's the one you meant you were using.
http://wiki.flatpress.org/res:plugins#bbcode
Click on the little picture there to see the syntax. It's very easy - you just add x=1 inside the opening url tag. I use it all the time now.
You can see it in action on the tutorial page I linked to above. See where you can see the small version of the "open new window" icon shown below. This method gives the user the option of opening the link in a new window or not.
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