Common sense says wherever the bags were sitting the longest presents the best opportunity for theft.
Several months ago, a friend and I traveled to Martinique, via a layover in Puerto Rico. Upon arrival at our hotel in Martinique, we each discovered we had been ripped off. My bag had a TSA lock on it, so it doesn't matter...they can still get in. They didn't leave a note either. Instead, my travel flat iron and my favorite perfume, just given to me as a gift, was gone. My friend's camera and jewelry were gone. The thief had to have opened up a zippered pouch in my suitcase to get my items, so it wasn't just rifling through the luggage, it was looking to steal things. This did not happen at the airport in Fort de France as we saw our luggage being loaded off the prop plane and taken right to the baggage area.
I never pack valuables in my checked luggage to avoid this kind of thing. I contacted American Airlines via e-mail and told my story, requesting they take some action. They "apologized" and deposited 10k miles in my account and did the same for my friend. While this doesn't replace your stolen items, it was at least something.
In hindsight, I probably should have sent a nasty gram to the TSA...