My question is, what is causing this and how to fix it?
The pairs of themes are not 100% the same… in the same way that the features of the WordPress software available at WordPress.com are not exactly the same as the out-of-the-box features you get from WordPress.org.
The WordPress.com versions of their themes often have extra code that integrates with the WordPress.com platform to provide additional features that are built into their platform, and which are not available in the open-source WordPress software from WordPress.org.
There’s really no way to “fix it”, other than:
1) Search to see if you can find a plugin that gives you the missing features
2) Look for a new theme that has the features you need already
Good luck!
Got it! Thank you! That really helped!