We have noticed that if you apply a Handling Fee / Service Price Adjustment and the mark up fee is not apparent on your website, the reason for this is.
WooCommerce is caching your shipping results.
Whilst testing your shipping we advise you to enable this option: Shipping Debug Mode or Debug mode
WooCommerce V 2.0
Go to: WooCommerce / System Status / Tools / Shipping Debug Mode
WooCommerce V 3.0
Go to WooCommerce > Settings > Shipping > Shipping options
When you have finished testing your shipping you can disable this option.