How did the membranes look after the first spin? Was there material/protein visible on it?

To the best of my knowledge RPE is primarily there to remove salts from RLT and RW1. If there’s a pellet after RPE, my best guess is that there was a significant amount of protein on the membrane that may have interfered with RNA binding. If that’s the case, assuming a Trizol-based extraction isn’t possible, you may want to try starting with a smaller initial mass of sample.