When the Migrate Data step is run in the Compatible Units Administration tool in ArcFM 10.1, compatible units in the System Favorites category are not included in the migration. Compatible units in the Compatible Units category are migrated correctly. These favorite categories are visible in the ArcFM System Favorites Manager Compatible Units tab.
This issue is caused by bug MM49732 in ArcFM 10.1.
Install the lastest patch for ArcFM Solution 10.1. This bug is fixed in ArcFM 10.1.1 and later releases.