Long story short, I took off on RWY 31L from JFK and was asked to hold 5000' for the full 10 mins before proceeding to FL340.
The FMS failed to recalculate a profile and deleted all the waypoint crossover times, speeds and altitudes. It also, obviously refused to engage profile mode. I was able to use LVL/CH just fine. At altitude I uploaded the flight plan again from the ACARS Menu and continued the flight.
Not sure if this is a bug so I thought I would let someone know.