HI, i had the same problem with blank component.
Fix is very easy.
From JoomSef main page go to Manage Extentions section and under installed extentions click on blankcomponent parameters.
Leave all settings as is and only change this one:
Ignore multiple sources -> no
After that your SEF links will point to where it should.
Example.
Non SEF url:
index.php?option=com_blankcomponent&view=default&
Itemid=244
will be converted to SEF using defaul component and Itemid (ID of menu item)
See it in action on my site (all 1st level menu links are Blank component)
http://freewarefiles.ru/