Hi Hugo,
While you mentioned that there is "no discernable pattern" for this issue, is there another computer with ArcGIS available to you, to determine whether this issue is reproducible?
When it comes to naming, I'm quite cautious and keep all three toolbox names the same (name & label & alias) and stick with alphanumeric characters (staying away from special characters like spaces, dashes & underscores). Similarly, I keep the ETL Tool names simple and identical (name & label). Then for my "first cut" of the Python script, I usually add the ETL Tool to a model and then export to Python.
Long ago, I ran into an issue where I could not invoke one of my tools. I noticed that it had the same tool name as another tool, but in a different toolbox. When I renamed the tool to a unique name, then it ran fine again. Unfortunately, I don't currently have the details for this issue, so I don't know whether this was an issue with ArcGIS Geoprocessing or whether I simply hadn't set all of the names/aliases appropriately.
While trying to reproduce this issue just now, I created two toolboxes named ETLToolbox and ETLToolbox2, each containing the two ETL Tools named mif2gmlETLTool and mif2gmlETLTool2. My Python script successfully invoked each ETL Tool in each of the toolboxes:
import arcpy
arcpy.CheckOutExtension("DataInteroperability")
arcpy.ImportToolbox("C:/data/ETLToolbox.tbx")
arcpy.ImportToolbox("C:/data/ETLToolbox2.tbx")
arcpy.mif2gmlETLTool_ETLToolbox("C:\\data\\province.mif", "C:\\data\\out\\province1.gml")
arcpy.mif2gmlETLTool2_ETLToolbox("C:\\data\\province.mif", "C:\\data\\out\\province2.gml")
arcpy.mif2gmlETLTool_ETLToolbox2("C:\\data\\province.mif", "C:\\data\\out\\province3.gml")
arcpy.mif2gmlETLTool2_ETLToolbox2("C:\\data\\province.mif", "C:\\data\\out\\province4.gml")
Hopefully something in this post might be helpful. If you have a reproducible scenario, then I'm sure Esri support would like to hear about it! (And so would I!)
Curtis Fast.
Safe Software, Inc.