The interaction of carbon monoxide molecules with atomic-scale platinum nanojunctions is investigated by low temperature mechanically controllable break junction experiments. Combining plateau length analysis, two-dimensional conductance-displacement histograms and conditional correlation analysis a comprehensive microscopic picture is proposed about the formation and evolution of Pt-CO-Pt single-molecule configurations. Our analysis implies that before pure Pt monoatomic chains are formed a CO molecule infiltrates the junction, first in a configuration that is perpendicular to the contact axis. This molecular junction is strong enough to pull a monoatomic platinum chain with the molecule being incorporated in the chain. Along the chain formation the molecule can either stay in the perpendicular configuration, or rotate to a parallel configuration. The evolution of the single-molecule configurations along the junction displacement shows quantitative agreement with theoretical predictions, justifying the interpretation in terms of perpendicular and parallel molecular alignment. Our analysis demonstrates that the combination of two-dimensional conductance-displacement histograms with conditional correlation analysis is a useful tool to analyze separately fundamentally different types of junction trajectories in single molecule break junction experiments.