PAUL TAYLOR  Hi, you dont need to have iTunes closed but as I think most people would recognise its not a good idea to modify any type of file while you are using it in another program , still I will take a look at this.

iTunes can automatically move files based on their metadata, but doesnt automatically scan files in folders, these can cause some issues for 3rd Party applications. But I have just finished a revamp of Jaikoz iTunes integration and this will be released later this week in Jaikoz 2.8.1.  
(Version 2.8)

WIZBIT  It does say in the Jaikoz help pages that:

"If you do update iTunes from Jaikoz it is recommended that within iTunes own Preferences you disable the Advanced\Keep iTunes Music Folders organized option because otherwise iTunes may move files that you are still working on within Jaikoz, it will do this if you are working on files that are within the iTunes music folder location."

So maybe give that a try and see if it works. :)  
(Version 2.9.2)