Problem building Arduino Uno firmware
Okay, problem found. The Vendor ID and the Product ID of the firmware was changed in subsequent non-factory firmware releases which prevented the Arduino drivers from recognizing it. The solution is to use either the drivers in the LUFA project folders, or change these lines in Descriptors.c

.VendorID               = 0x03EB, // Atmel
.ProductID              = 0x204B, // LUFA USB to Serial Demo Application


to this

.VendorID               = 0x2341, // Arduino
.ProductID              = 0x0001,


Hope this helps someone in the future.