I recall Matt and Steve saying that Fleet boxes were going to be discontinued, but I have not seen anything about discontinuing Squadron boxes.  I suspect this is temporary and due to the change in miniatures production facilities.  Mongoose Infantry (Mongoose's demo team) members aren't being sent what they are owed either.
I have seen several sources for Squadron boxes, including ADB, FRP Games, NWS-Online, and The Warstore for starters. 
FRP Games has Fed, Klingon, and Kzinti squad boxes, though supply is low.
ADB has a good selection.
NWS-Online has a good selection, it appears.
Warstore has a decent selection as well.