In a WPMU install there is no check box for “Organize my uploads into month- and year-based folders”

Instead you need to do the following:

network dashboard > my sites > sites

then edit each site, select site settings

then scroll down to “Uploads Use Yearmonth Folders”.
1= yes year/month,
0 = no year month, instead upload to /siteid/files/

Thanks to http://premium.wpmudev.org/forums/topic/how-do-i-turn-on-the-check-box-for-yearmonth-folder