Hello @RebeccaWatson1 @Javier_Pintos
Thanks, I was asking about DI and ArcFM Server 'cause in our case we have it (so I wanted to rule out that it was related).
In our case it has been similar, some environments have already been upgraded to 10.9.1 and work normally so it is not a widespread problem. But if it has happened to you, it means that it is reproducible under certain conditions (?).
In the session with ESRI support it was raised similarly, we think it must be the publishing service (PublishingTools - PublishingToolsEx), so we stop - start it, compared with another environment in 10.9.1, and they are the same, deleted and created, replaced the xml file etc. but still not fixed.
In our case the environment is on a single server with Windows Server 2019 Standard, and the installation is on drive C (C:\ArcGIS\Portal, C:\ArcGIS\Server, C:\ArcGIS\arcgisportal and C:\ArcGIS\arcgisserver), using a AD service account. The server had first 10.7.1, later upgraded to 10.9.0 where it worked normally, and finally upgraded to 10.9.1 where we have the difficulty; I share this information, maybe its useful to rule out options and find a solution.
With ESRI has not yet been able to locate the issue, but if I have any information I will comment here.
Regards.