I ran into an issue with WP E-commerce recently where the shipping options appeared to be unchecked every day that we went to go and look at them. Turns out it was a line in one of the shipping files that reset the shipping array to just “shipwire” which made it appear as if someone was turning off shipping every day (or a cron job, in this case).

Read about it here: https://wordpress.org/support/topic/upgrade-to-43-and-problems-with-shipping-calculator

Anyways, I created a script to monitor changes to custom_shipping_options and thereby found out what the issue was. Here’s the code, hope it helps.