There may be some differences between what Minion Reindex reports and what SSMS reports for fragmentation levels.  MR will always take the maximum fragmentation reading that it finds from all levels (partitions, leaf or non-leaf level). 
 
There are a couple of ways this could happen:
 
Let’s say that you have a table with multiple partitions, and each one has a different level of fragmentation.  MR will take the highest one, whereas SQL Server may display just the most recent partition.  (This isn’t guaranteed, it’s just our educated guess as to the behavior within SQL Server.)
 
Another way, is if you have the system set for DETAILED fragmentation collection.  In this case, you’ll get all levels of any given index, and MR will take the maximum fragmentation it finds, whereas SSMS always reports on only one level.  So, you could have the leaf level that is 5% fragmented, and some non-leaf intermediate level fragmented at 78%. 
 
Note: You can investigate where the readings are coming from by saving the raw fragmentation statistics for all tables, or for a single given table. Just set the LogIndexPhysicalStats column in either settings table (Minion.IndexSettingsDB or Minion.IndexSettingsTable).  This will save the raw DMV statistics to the Minion.IndexPhysicalStats table for your inspection.  Note that this table isn’t part of the delete routine, so you’ll have to manage it yourself.