Hi, what you exactly mean, the pagination does not work in article the same way as it didn't work never in article. As it is not possible - for the pagination, you need to transfer GET parameters in URL (or POST or sessions parameters) but you are inside the article, so every parameter will be set for the article not for the plugin inside the article.With the old release of PG all worked fine...
If you need pagination, you should use the component - as in component the pagination can be fully managed and Phoca Gallery can get the information about the page and display it. When it is a plugin, it is inside the article, and there the rules of the article are valid - so inside the article - com_content component you cannot manage it by other component e.g. by com_phocagallery.
So then as Benno wrote, this needs to be customized but not in Phoca Gallery, but in Article, so it somehow influences the plugins inside them and display different pages of plugin output
Jan