Alternate least squares (ALS) reconstructions of the infrared (IR) spectra of the individual layers from original automotive paint were analyzed using machine learning methods to improve both the accuracy and speed of a forensic automotive paint examination. Twenty-six original equipment manufacturer (OEM) paints from vehicles sold in North America between 2000 and 2006 served as a test bed to validate the ALS procedure developed in a previous study for the spectral reconstruction of each layer from IR line maps of cross-sectioned OEM paint samples. An examination of the IR spectra from an in-house library (collected with a high-pressure transmission diamond cell) and the ALS reconstructed IR spectra of the same paint samples (obtained at ambient pressure using an IR transmission microscope equipped with a BaF2 cell) showed large peak shifts (approximately 10 cm−1) with some vibrational modes in many samples comprising the cohort. These peak shifts are attributed to differences in the residual polarization of the IR beam of the transmission IR microscope and the IR spectrometer used to collect the in-house IR spectral library. To solve the problem of frequency shifts encountered with some vibrational modes, IR spectra from the in-house spectral library and the IR microscope were transformed using a correction algorithm previously developed by our laboratory to simulate ATR spectra collected on an iS-50 FT-IR spectrometer. Applying this correction algorithm to both the ALS reconstructed spectra and in-house IR library spectra, the large peak shifts previously encountered with some vibrational modes were successfully mitigated. Using machine learning methods to identify the manufacturer and the assembly plant of the vehicle from which the OEM paint sample originated, each of the twenty-six cross-sectioned automotive paint samples was correctly classified as to the “make” and model of the vehicle and was also matched to the correct paint sample in the in-house IR spectral library.