I had the same problem, I fixed it by using the Basic Editor of the GCP/MTP Manager and marking each GCP on three images, hit Reoptimize, after that they started to show up in the rayCloud and the Automatic Marking option was available, hit it, and more images showed up to be able to be marked with the GCPs, I marked few more, hit Reoptimize, and I confirmed in the raycloud graphic the elevation of the model was fixed with the GCPs. some screenshots below.
model relative to GCPs before the fix:
model elevation before the fix:
Basic Editor:
verifying model elevations after fix (average ground elevation is around 435m), GCP #13
elevation on a model´s point closed to GCP #13