I am not familiar with your specific application, but I do know GPS receivers and the PPS output has sometimes some serious phase jitter... many times more than a good signal generator. If you use a PPS from GPS as a reference to the DPLL obviously the thing gets confused.
Even filtering the PPS is not an option because the jitter of GPS PPS is not gaussian but depends on satellite constellation changes and can do sudden jumps. I recommend to lock in the the OCXO then use some seriously heavy filtering on the GPS PPS (hours) or better use RTK or DGPS (differential GPS with satellite provided corrections).