@lisainchicago: Something you could do is to save the epubs generated by the manual conversion and the email conversion and compare them. You might At the least you will find what the differences are and maybe work out some defaults you can use for the conversion. Plus you may be able to see what the source of the conversion is.
If it is happening consistently, you can run calibre in debug mode and post the debug log for us to look at. Hopefully it will show what is happening.
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