This plugin is works with WooCommerce product image lightbox.
If you deactivate our plugin, then the content that you inserted into the tabs also deactivated, so I suppose not the plugin, but the content is wrong.
Please try to remove every special content from the tabs (especially Google Maps), maybe this is in conflict with WooCommerce lightbox.
In our site you can see that lightbox and tabs work together without problem.
We have successfully tested the latest versions together: WordPress 4.1.1, WooCommerce 2.3.8 and Woocommercer Custom Tabs 1.0.17. The lightbox works without problem using these versions too.
So something is wrong in your environment, maybe tab content, but we have not got enough information to find the exact reason.
I hope this information is help you to find the problem.