After manually entering all of my settings from a backup configuration, I believe I found a more concrete answer than 'something in the upgrade path'. I have a multi-wan setup and do load balancing and prioritization across each link. Everything on the clean installed worked fine until I had loaded all of the rules in (which is where outbound gateways are defined). It seems that between the April 17 2012 snapshot that I was running and last weeks, something changed with how internal IPs and directly connected networks are routed when the default rule for an interface does load balancing. I believe the change occurred in a more narrow timeframe as I have had this issue on other snapshots I tried as well, prior to list week, including a Sept 2012 snapshot.
I am not sure how many others have come across this issue, or if you always needed a rule per interface to handle internal/direct connected networks and the snapshot I was using had a bug that ignored that, but it would be good to know what changed in regards to that and why.
Thanks all for reading about my troublesome weekend messing with pfSense snapshots.