Using .raw vs Using .mzml (converted from same .raw using msconvert) yield different in msdial v4.9.22

[ayaazuddin]

For context: New to metabolomics and msdial. Trying to use the msdialconsole for metabolomics. Since msdialconsole v4.9.22 does not allow .raw files as input (or if it does I keep getting an error), I used msconvert to convert the .raw to .mzml and then used the console. Unfortunately I get varying results.
I crosschecked the parameter files, played around with different parameters of peak picking is msconvert but I keep seeing differences.
Differences being some mssing metabolites in the Height file and differences in values of particular metabolites in the two runs (the two runs being .raw done in msdial v/s .mzml done in msdialconsole),

Any ideas on what could be the cause? Is it just because of the them being different formats and there is nothing I can do about it?