If you’re using any kind of paginated element in a custom layout, you want to make sure and use the second method of applying the custom layout to your homepage.
- Go to Settings > Reading > Frontpage displays and select “your latest posts.”
- Go to Appearance > Theme Options > Content > Homepage and select your custom layout there.
From what I know, WordPress has odd issues when you try and paginate anything from a static frontpage. I’ve never had much luck with it in general without little hacks and what not, but have never found a solution that works for everyone.