WordPress Version: 3.4
WordPress SEO Version: 1.2.3
I'm using WooThemes (Canvas) and I have my Home Page configured in Magazine mode.
Last week I made the cut over to your plugin and only just now noticed what appears to be an incompatibility between the WooThemes magazine mode and your Plugin.
Additionally, the rel="prev" and rel="next" are missing as well.
My guess as to why this is happening is because in order for the WooThemes Theme to show the Homepage in Magazine Mode, you have to go into WordPress settings and configure the Home Page to point to a published page on the site. That Published page then needs to be set to the Magazine Mode template. My guess is that is why your plugin is picking up the canonical as /2/ vs. /page/2/ because it see's the home page and later subpages as a single post vs. the home page with sub pages.
I confirmed this when I set the home page to the Latest Posts and sure enough, all the correct canonical urls were then picked up from your plugin and displayed properly as were the rel="prev" and rel="next" links to the front and back pages.
Obviously this feels like a WooThemes bug in their theme however my guess is they will have no interest in fixing this since it's your plugin grabbing the canonical and displaying it. Since your theme is closely aligned with Woo, I'm hoping you might have a hotfix I could use where your plugin looks at the home page, determines if the page set is configured to magazine mode then set the canonical appropriately.?.?.?
Thank a lot. I appreciate your support.