I definitely think it was most likely that you were disrupted from REM sleep by the thunder. Actually, frustratingly enough this happened to me about an hour ago when I was napping. My phone rang and woke me up, I hit the silence button on it and went back to bed, immediately getting vibrations and just started to LD and then my phone beeped really loud that I had a message and woke me up and I couldn't ge back into he groove b/c i was too disrupted by then, darnit. Oh well. Try the WBTB method to induce lucids, sounds like it would be good for you.