I have problems with permalinks, it runs only in default mode for mapped domain.
1) WP 3.7.1, subdomain mode, 3 sites: a) mainwebsite.ext, b) sub1.mainwebsite.ext, c) domain2.ext -> Permalinks runs fine on a) and b), doesn runs on c)
When permalinks is active the error is "Page not found" in the content page area.
Looks here for more info: http://stackoverflow.com/questions/21479095/permalink-problems-with-wordpress-multisitesmultidomains
Thanks for your support.