when GSX begins the passenger loading process - the payload and cargo entries I placed get erased and start at zero.
GSX doesn't have any control over the FS Labs payload, and it never tries to set it directly. The only thing GSX does, is to set a variable telling the airplane how many passengers are boarding, the rest is entirely up to the airplane.
Now, while its entirely normal you would see the *passenger* payload go to zero when boarding start (that's exactly what is supposed to happen), it's not normal the *cargo* payload would also go to zero but, again, we don't touch the payload in either case so, you better ask FS Labs about this.