the following error is logged onto the python prompt for many scripted modules (AtlasTests, Charting, etc.):
"qSlicerScriptedFileWriter::setPythonSource - Failed to load scripted file writer: class %1 was not found in file %2"
but somehow these messages don't appear. It is done in qSlicerScriptedFileWriter::setPythonSource.

className in these cases is always empty, because it is called with an empty argument for className (see call stack below) from the function qSlicerScriptedLoadableModule::registerIO() like this:
bool ret = fileWriter->setPythonSource(d->PythonSource);

It appears for me if I add a setup() method in the python class of a scripted module, in my case the DICOM module. I worked around it by adding a dummy class DICOMFileWriter.

Probably we shouldn't log an error if a scripted module doesn't have FileIO capabilities, as it is not an expectation. Also it is strange that the error is logged but doesn't appear. Maybe the interactor is not fully initialized yet?