A USB-IF specification requirement is to never drive the USB pins when they are not connected to the bus. In order to meet this spec requirement it is always recommended to use a Vbus monitor circuit in self-powered devices.
Please go through 6.3 Wakeup/Resume of TRM for more information on wakeup pin and its usage.
Please look at http://www.cypress.com/?rID=12961 for complete detail on why VBUS monitoring is needed.
As to the use of WAKE pin to make the chip enumerate in your scenario. It might have to do with hardware issues. Does your crystal meet the parameters specified in FX2LP datasheet?
When you run into the non-enumeration scenario is there oscillations on the crystal pins?