Combining insights from machine learning and quantum Monte Carlo, the stochastic reconfiguration method with neural network Ansatz states is a promising new direction for high precision ground state estimation of quantum many body problems. At present, the method is heuristic, lacking a proper theoretical foundation. We initiate a thorough analysis of the learning landscape, and show that it reveals universal behavior reflecting a combination of the underlying physics and of the learning dynamics. In particular, the spectrum of the quantum Fisher matrix of complex restricted Boltzmann machine states can dramatically change across a phase transition. In contrast to the spectral properties of the quantum Fisher matrix, the actual weights of the network at convergence do not reveal much information about the system or the dynamics. Furthermore, we identify a new measure of correlation in the state by analyzing entanglement the eigenvectors. We show that, generically, the learning landscape modes with least entanglement have largest eigenvalue, suggesting that correlations are encoded in large flat valleys of the learning landscape, favoring stable representations of the ground state.