Not sure if you've tried this but try setting the GML reader parameters to 'ignore application schema'. It sounls lke be that it's looking for some xsd files which aren't there. It's a fairly common annoyance with the GML reader.

 

If you want the proper schema to be used then make sure the xsd schema set referenced in the GML file is accessible.

 

I assume that QGIS has some logic built in to try and find it and then just use a default if it can't find it. With FME you must explicitly tell the reader to ignore it - This is important because if a workspace is shared without the xsd schema then the workspace can produce different results and can cause massive headaches for various support personell.

 

If you want FME to ignore the schema by default you should be able to save your reader settings as default for next time.

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