Thank you for writing us.
Could you please tell me the way to reproduce this problem? Is there any special actions you did during the download process?
This problem was also present in Ver 2.
Thank you for these details.
Is this possible to provide us with the file link?
We plan to release Mass Downloader 3.1 Beta 1 in couple of weeks.
We improved the code working with extension removing. This problem should be fixed.