Next beta for eagle import are online.
Please check this, choose the maxdrilldiameter to 1.1mm and the new cut diameter to 2. If u have holes they 1.5mm, then you get a warning thats impossible to mill.
Also i include a this routine http://jsfiddle.net/xpix/fz5t1rwn/ to make holes as arcs. Short, user can decide … drill holes up to Xmm diameter, the rest will mill (if possible).
Happy milling 
http://jsfiddle.net/xpix/fz5t1rwn