@Emanuel V that is very surprising, and I’d dare say would even constitute a bug. I have never seen an instance of a GL plugin not running in any context, unless the plugin had code to exit early under certain circumstances, which is possible.
Are there any differences between the scripted load/save and the UI action? A different form perhaps? Also, is this a closed third party GL plugin? I wonder if you can view the code to see if it may be be exiting somewhere.