For WSS V3 we created a fix so that after a security update the workflow will start automatically. With SharePoint 2010 we will have the same scenario and we will need to do the same steps we have since the fix for the earlier version.
It means we need to run stsadm -o setproperty -pn declarativeworkflowautostartonemailenabled -pv true also with SharePoint 2010.
All the information in the KB article 953289 is valid also for SharePoint 2010!
953289 A declarative workflow that is configured to start automatically when e-mail enabled items are created does not start automatically after you install Windows SharePoint Services 3.0 Service Pack 1
SharePoint 2010 SPWebService.DeclarativeWorkflowAutostartOnEmailEnabled Property