Doing moves *within* MC has distinct advantages. The biggest one is that MC retains all custom library fields (even ones that aren't in the file's tags), playlist entries, etc. The one of these that you will possibly notice the most is Import Date.
Every time you move a file outside of MC, and MC detects it, it thinks two things have happened: First, the old file is gone. So it deletes that entry from it's database. Second, a brand new file appeared in a new place, so it imports that file fresh and new. With a new import date! So every time you move files outside of MC, MC thinks they are brand new. This screwed me up a good bit until I figured it out.
Now I do all of my moves from within MC. If they are really big moves, I do them outside of MC, then use the Rename, Move, and Copy files tool in UPDATE MODE to tell MC that I moved them externally. That way the database stays consistent and nothing with the metadata changes. Including the import date.
Brian.