AE startup script and ME watch folder

Hi

I'm trying to load xml files from a weather api into a composition in After Effects and spread several values from the xmls on several layers in this composition. I'm doing this with a script in the startup script folder, as i want to execute it when After Effects is starting. In After Effects this solution is working pretty well but if i want to render this project through watch folders with the data from the weather api in Media Encoder the renderprocess won't start.

So my question is, is it impossible to use startup scripts if i want to render with watch folders in Media Encoder? Or is there something i have to implement into the startup script to make it work?

Hopefully someone out there can help me