If you have a custom MAPI account (apart from SMS, MMS, ActiveSync and Hotmail) to add to FlexMail you need to use a following registry tweak.
If you add a string value named AddMAPI to [HKEY_CURRENT_USER\Software\WebIS\Mail2\Services] with comma-separated names of accounts you want to add to FM it will load them on the next restart.
This article is about FlexMail 4 only.