A scintillating lithium indium diselenide (LISe) single crystal has recently been found to exhibit an eight-fold increase in its apparent light yield within 80 µm across the surface when excited by cold neutrons. The cause of this observation is currently unknown. In this paper, we report on our investigations to explain the previous observations of nonuniformity in scintillating LISe. Using a two-photon interband excitation instrument, we found that the lower and higher light yield regions “scintillate” at peak emission energies of 1.98 eV and 2.4 eV, respectively, and no region investigated exhibited both. Volumetric evaluation found a relatively uniform scintillation response in each region, verifying that the relatively flat spatial resolution of LISe substrates of varying thickness applied to neutron imaging is not from only near-surface scintillation mechanisms. Raman investigations indicate that the vibrational modes of the scintillating LISe substrate is somewhat different than that reported in literature, but no apparent difference between the two regions was observed. Using ToF-SIMS in each region, we found that the 1.98 eV emission region contains additional lithium, which is consistent with neutron absorption results. We suspect that the sharp transition in peak scintillation emission is due to a change in the charge state of Li-In antisites, but that the observed scintillation light yield and emission energy change is not directly correlated to crystal color. Qualitative comparison between the observed noise in the two-photon “scintillation” spectra indicates that the light yield between each region is not due to the quantum efficiency of the CCD used during cold neutron interrogation experiments, but an actual change in the light yield.