Hi Dan,
The upgrade process did not go well and there is issue with DFOs of the Application. Below are the few approaches you can take.
1. Run a repair install of the patch 1. If this step fixes the problem, I bet you are a very lucky man.
2. Add a new SIA with different name and port number. Even this is not bad, but you will have to re-configure any server setting you did previously.
3. Roll back 4.1 and patch 1. Restore the backup of CMS and filestore. Re-run the installation.
4. Create a new 4.1 SP3 Patch 1 system. Migrate the content from the current box to the new install.
Unfortunately I am not aware of any simple way of fixing this. Please do update the thread if SAP support comes up with a better solution.
Regards
Chinmaya