Hi Takayuki,
I have been monitoring this thread for the last three weeks (actually, it feels like much longer), because I have the same problem: uploaded files are uploaded all right, but they are not deleted from the server.
Because you did not receive a reply on your questions, please allow me to "revive" this question (rather than starting a new thread about the same issue).
I use CF7 3.3.3. The site URL is http://www.bcstar.nl/0. You will find a page on which CF7 is used with file uploads here, for example: http://www.bcstar.nl/0/?page_id=729.
The uploaded files are stored in http://www.bcstar.nl/0/wp-content/uploads/wpcf7_uploads; all standard, so to say.
By the way, the site is hosted on a Windows server.
Hope that you can provide a solution for this!!
Thanks and best regards,
Henk Barreveld