What browser are you using? I'd guess Firefox, Opera or Konqueror. There are a bunch of others it could be, but those are fairly common ones.
For Firefox, go to the Edit menu, then Preferences then there should be a Content tab. Under Content, there should be a Block pop-up windows checkbox. Make sure it's checked and see if that solves the problem.
If you a different browser, let us know which one and we'll see if we can help get rid of those pop-up windows.
BTW, Gentoo is a fantastic distribution of Linux.
Has it been a few days since I replied to your thread? Don't panic! I'm usually very busy and may forget a post if I'm extra busy (or it might just take me a while to be able to do a decent reply). If you still need help and are awaiting my reply after a few days, PM me about it.
When posting what errors you get, please give the full message. It makes helping you much easier.