What process did you use to rebuild the network? After the rebuild, did you run the ArcFM Object Convertor tool on the database?
After rebuilding a geometric network, all of the feature classes are left as ESRI objects. My top guess is that you need to run the ArcFM Object Converter tool on the dataset that contains the geometric network, and convert to ArcFM or Designer objects.
If objects are not converted, autoupdaters can't run, which would likely explain the issues you are seeing.