Another thing to check is if any applications still have a hold on the file.
Had some issues with MoveFile. Part of my permissions problem was that my script opens the file (in this case in Excel), makes a modification, closes it, then moves it to a "processed" folder.
In debugging a couple things, the script crashed a few times. Digging into the permission denied error I found that I had 4 instances of Excel running in the background because the script was never able to properly terminate the application due to said crashes. Apparently one of them still had a hold on the file and, thusly, "permission denied."