Hi there!
Could you please share a copy of your site’s System Status? You can find it via WooCommerce > Status.
Select “Get system report” and then “Copy for support”. Once you’ve done that, paste it here in your response.
Regarding syncing orders, WooCommerce Square extension never had this feature. That said, there is an existing feature request regarding this topic in the ideas board.
Please vote (optionally, comment) on the topic so that it gets more visibility. This is where developers go to look for future plugin features and improvements.
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Regarding the pending payment orders that are created, can you please post screenshots of the order notes here?
If you don’t already have a screenshot service installed, you can try https://snipboard.io or http://skitch.com/. There is also a walkthrough guide here: https://en.support.wordpress.com/make-a-screenshot/. You can share the direct link to the image as a response to this topic.
[Please redact any private details, including address, name, email address, transaction details, etc]
We haven’t heard back from you in a while, so I’m going to mark this as resolved – if you have any further questions, you can start a new thread.