I have the same issue.
I check the checkbox for the minimum threshold, set the minimum amount to 200.
The product is priced at 2, yet the fee still is applied.
I am updating all plugins related to WooCommerce on a weekly basis – maybe this is something that has worked in the past, I can’t know because I didn’t use this feature before now. I am using WordPress 4.9.7 and version 1.4 of WooCommerce Add Custom Fee.