Strangest thing - I have a homepage with multiple loops that worked perfectly until I upgraded the SEO plugin and then it broke. Each loop displays the first post it is supposed to, and then X number of recent posts depending on the number X set in the reading menu.
I saw an update today so I applied that in case it was a fix and it's still broken.
It would be great if we could understand what happened here as I don't want to switch to another SEO plugin. I'm going to have to try and track down a previous version so that i can still use it.