If you have multiple instances of your store connected to your Shiptheory account, and shipments from the 2nd store are not coming through Shiptheory, you'll have to make sure that the shipment IDs are unique.
To verify this, login to your 2nd store admin panel and go to (Magento)Sales -> Shipments, and copy one of the Shipment IDs you can find there. Go to your Shiptheory dashboard and enter the ID and hit Enter/Return key. If it returns another shipment (from your 1st store), then that's the reason why the 2nd store's shipments are not coming through.
What do I need to do now?
You'll need to set up different IDs for your 2nd store. You might need to contact your developer to accomplish this.
Still having troubles?
Feel free to contact Shiptheory Support.