I'd guess it's actually a fignewton of the OS and "lazy" deallocate/reclamation that the memory is flagged as clear but as long as the application is running there's no opportunity for the OS to actually release it.
Try creating a memmapfile object instead of a disk file -- it may have a better chance of releasing or reusing memory and likely will have better performance besides.
It's always worth a query to official TMW support at www.mathworks.com; particularly if you can cut your code down to a bare-bones app that creates the issue but is small in size--it may be that simply the file creation/deletion alone will demonstrate the issue I'd guess.
