This issue happens to me too, but with Finder (using TotalFinder). I open a folder using Alfredv2 and then I open another folder and the second Finder window opens in the background of the previous opened window, so it's very frustrating when you want, for example, copy some files, open destination folder and paste them just using the keyboard. First the finder window appears in the foreground and one second after jumps to the background. I didn't have this issue with Alfredv1.
I'm using Alfred v2.0.2(178) with PowerPack license. My OSX version is Mountain Lion 10.8.3.
If you need more information, just let me know.
Thanks for your support.