Timber buildings, including hybrids, are increasingly popular due to their beneficial environmental aspects. During 2023-2024, the authors had a unique opportunity to perform ambient vibration testing of two six-story buildings with identical timber structures placed on top of different types of concrete substructures and with varying soil conditions. Ambient vibration tests were performed twice during the construction of each building. Finite element models were created for each vibration test, and their parameters were updated simultaneously to accurately simulate the building's natural frequencies and corresponding mode shapes. The model updating process was facilitated by training four surrogate models to represent the four finite element models corresponding to the two buildings and the two construction stages. The updated models were used to investigate the effects of the in-plane shear stiffness of cross-laminated timber (CLT) walls, soil-structure interaction, moisture content, and non-structural walls on the dynamic properties of hybrid timber-concrete buildings. The results showed nearly identical dynamic performance of the two buildings, suggesting that the differences in sub-structure and soil conditions do not affect the natural frequencies and mode shapes. A sensitivity analysis revealed that the in-plane shear stiffness of the CLT walls is the most significant factor affecting the modal properties of the two buildings.