I have found a solution that worked for me (iTunes 12, Windows). I had a few films that I had imported as home videos, but despite changing the meta tag to film they still remained in the home videos folder on my hard drive.
I tried to use the File > Library > Organise Library menu but the checkbox to organise files in the iTunes Media folder was disabled (I already had the automatic organisation enabled in settings).
- Open the advanced settings tab (Edit > Preferences > Advanced, you may need to press the alt key to display the menu bar).
- Uncheck the checkbox "Keep iTunes Media Folder Organised"
- Press okay.
- Repeat steps 1 and 2, but this time checking the checkbox again.
- When you press the okay button a progress bar will appear in a popup (before the settings popup closes, it may appear behind the settings popup), wait whilst your files are moved the their correct locations based on their metadata.
Note: This may mess-up your library file structure if you use anything other than the default iTunes organisation.
Also check that you have "Copy files to iTunes Media folder when adding to the library" checked in the advanced settings tab.
You can check that the files have been moved, by right clicking on a film that was in the wrong place and clicking "Open in Explorer" - it should now open the file in the correct position.
I found that I had to repeat this process every time I add a new film which didn't move automatically.
TL;DR: Uncheck and re-check "Keep iTunes Media Folder Organised"