Please match the schematics against the hardware guidelines provide from Cypress. AN70707: http://www.cypress.com/documentation/application-notes/an70707-ez-usb-fx3-fx3s-hardware-design-guidelines-and-schematic
Next check the PMODE pins, and ensure that they are set as per USB boot.
Is it happening on one of your boards, or you see the same behavior on multiple boards?
Thanks for your valuable comment. Given that there is nothing else to look for, we digged the hardware and problem turned-out to be a crystal/oscillator problem.