Singlet-triplet gaps in cationic organic dyes are central to many photochemical applications. These typically involve solvated absorbers subjected to poorly characterized environmental perturbations (and spectral shifts). Here we experimentally probe "intrinsic" singlet-triplet gaps in isolation and at T ≈ 5 K. We study two prototypical systems, protonated proflavine and acridine orange, fluorophores with singlet ground states which in solution also have significant triplet quantum yields. Using a two-color, pulsed laser photodissociation (PD) scheme combined with cryogenic ion trapping in the gas phase, we determine vibronically resolved NIR absorptions of metastable triplet state cations tagged with individual helium atoms. Photoluminescence (PL) spectra of the same cationic species deposited into inert neon matrixes allow us to estimate the separation of ground (S0) and lowest-energy triplet (T1) states. Using the same methods, we also measure the corresponding S0-S1 respectively S1-S0 transitions, again resolving vibronic features and locating 0-0 origin bands. TD-DFT calculations using the ωB97X-D functional and cc-pVDZ basis set as well as vertical Hessian modeling as implemented in FCclasses3 satisfactorily describe vibronic features, thus allowing us to assign the experimental spectra as S0-S1/S1-S0, T1-T3, and T1-S0 transitions. At this commonly used level of theory, however, S0-S1 and T1-T3 energy differences are not predicted to be within chemical accuracies. Furthermore, calculated S1-T1 energy gaps are even less reliable.