When I invoke the tool with "msconvert.exe file.raw" I get a file.mzML with some tags missing after the last spectrum, namely </spectrumList>, </run>, </mzML>, and </indexedmzML>. This happened for all the RAW files I tried.
The error I get is:
[ReaderFail] [ThermoRawFile] Failed HRESULT returned from COM object: 5
Error processing file file.raw