Some items in my auto-charging subscriptions were charged tax and others aren't. Why?

The tax is charged on subscription renewals based on the tax configuration which was on the product when the customer placed the initial subscription order.
To update the taxable property on existing subscriptions, we recommend you to just recreate these subscriptions in Seal Subscriptions > Subscriptions > Add subscription manually and then delete/cancel the old ones. The new subscriptions will be created with the taxable property, which is currently set on the products in your shop.