Hi there,
Kind of the same issue here so I share with hope it can help.
I realized that starting from cart page, when customer add another product after navigating to shop and products pages and then come back to cart, free shipping method is not available anymore. However, if a product is removed from cart, free shipping option comes back as cart updates after modification.
In PayPal settings, issue disappears when PayLater messages option is disabled. Maybe behavior of messaging in products pages is key here.
Regards,
Kevin
