As a test I launched an entire inner system worth of satellites one at a time (6 for Kerbin, 3 for Mun, 3 for Minmus, 3 for Deep Space end points - so 15 separate launches, each with a unique name) and never got the exploding ship bug. Then I sent up a single ship with 6 satellites on it to Dres. Before I had the 6th one in orbit I'd corrupted the save to the point where it wouldn't load. I think RT2 may have a problem with how the names change when you split ships into multiple satellites while they are connected into the network.