I just fired up my system and added Waves Saphire to the master bus of both a new and existing project without any problems.
The existing project contained instances of Brainworx Hi-Pass Filter, Maag EQ3, Waves L1, Sonitus Reverb, Waves GEQ and Waves C1.
No theories on the cause of your issue (although a conflict sounds likely), but maybe this will help you narrow down the list of potential suspects.