When working with Microstrategy there is a chance for the metadata to become corrupt. There are 2 types of errors; Physical or Logical. Scan MD is the tool to recover from logical inconsistencies where MD Doctor fixes physical errors.
The recommendation is that Scan MD be run a minimum of once a month to eliminate the inconsistencies. This is especially true with a large number of developers all working within the same project. One good example of how this corruption happens is if I am changing an attribute and have not saved it and someone else updates the schema it can cause the Atrribute definition in the metadata to become corrupt.
I have used an older version of Scan MD which tends to display a ton of errors some valid some not. I have been reading up on a new version which was released with Microstrategy 9 and apparently eliminates these "false" errors. This new version can be used with older versions of Microstrategy.