Yes the popup blocker can be quite sticky to work around. Part of it has to do with the fact that its plugin asking to open a new window, another part has to do with how click new windows are requested and also the amount of code that is run before the new window request is made impacts the popup blocker's decision as well.
I spent a fair bit of time investigating and its getting around popup blockers isn't really something the creators want you to do easily. My idea is to only use new windows if you really need to. Most people get the Back button concept and will come back to your site if its worth it.
It looks like there's no easy answer. Most people have no clue how to disable a pop-up blocker so if it doesn't work right away all of the time people will just ignore it. That's not good.