Another update in case anyone is interested...
I picked up my commander last night after the 2nd fix and drove home with no problem. This morning, I didn't even make it out of the driveway and the light comes back on and I only have 3rd gear again. I went straight to the dealer and they fixed it while I waited. They also better explained the issue for me. This is what they told me, but I'd like to get some of your opinions...
There is a wire harness that connects to it's fuses at the driver's side of the support bar above the engine. The harness goes over the bar and joins with some other wires before traveling down toward the transmission. The first time I had the problem, the harness was loose at the transmission-end. The second time, there was a cut wire right at the support bar by the fuse connection that was making contact with the bar and causing a short and blown fuse. The third time they fixed it (this morning), they said that there was a loose connection in the same harness, but this time at the fuse-end, not the transmission end. It appears that all three of these had the same cause - the harness is pulled too tight. Apparently it is the same harness (and same engine compartment set-up) as the Grand Cherokee, but in the GC the harness goes under the support. For some reason, they used the same harness in the commander but routed it over the support instead of under it. I asked if they could just re-route the harness under the support, but they said they didn't want to do that without finding out first from DC engineers if there is a reason for it being routed over the support instead of under it. They checked several other commanders, and they all have the same set-up.
So according to the dealer, this is the first time they've seen this problem, but they anticipate that they will have more like it because they think it's a design issue, not just something wrong with my commander. They said if it happens again, they'll replace the harness and see if that works. Since this is the third time they've fixed it, I wonder if they are telling me it's a commander design flaw only to disuade me from requesting another car. I'm a skeptic.... hopefully that's not the case.