I've just had a play with this and Alfred is actioning the buffer items in the order you see, so the behaviour may be caused by the destination software.
i.e. if I have pdf1, pdf2 and pdf3 in the buffer and use "Open With..." in Preview, I see that Asks OS X to open pdf1 in Preview, then pdf2 in Preview, then pdf3 in Preview.
One thing I remember a long time in the past was an odd behaviour where some software wasn't correctly buffering up the open requests and would buffer up while the app was launching, opening these ones after the app had launched and dealt with the latest open with commands.
Try using the buffer with the destination app open and see if you get different behaviour.
Cheers,
Andrew