I think I might have found the problem. When I look at the fuse box for the 30 Amp large main fuse. This is the one second from the top not the top one which is a spare 30 Amp fuse, I noticed that I can only clearly see one connector, the right one. The left one must be inside because when the fuse is inserted there is a connection, but it appears to be pushed in far enough that I can't see it. I've looked at all of the other fuses and I can easily see both connectors inside. I'm assuming that if the left side connector is not making good contact with the fuse, a little vibration would be all it would need to cause an arc, loss of contact and overheating.

Before I take my bike into the dealer and ask them to replace the fuse box under warranty, I was hoping someone else could check their 30 Amp fuse receptacle on their Speedmaster to see if they can clearly see both connectors.