Are the fields being blanked bound to a secondary data connection?
Secondary dataconnection values do not get sent with the final form xml. Only Main dataconnection values. If you need secondary data connection values to be saved and sent, they need to be copied into a Main dataconnection field.
Another thing which has got me in past is if I use Rich Text or HTML format for a manually created Outlook email in script.
If a user has Microsoft Word as their Outlook editor, this seems to do weird things to certain table formatting - like it just disappears! Not sure if this is your problem though.