Nintendo 3DS developer NekuSoul has made some updates and is now releasing version 2.3 Beta 2 of the 3DS Video Converter.  There have been some bugs fixed from the last release and you can view the full changelog below.

"FEATURES:
Multiple File Conversion
Fast Conversion using Threads
Drag'n Drop
Supports multiple Cores
Supports 3D and 2D Videos
Changeable Quality
Output-Folder can be set
Progress-Bar in Taskbar (Win7 only)
Renaming Videos to automatically fits into 3DS's naming scheme
Automatically cuts Video into multiple 10 minutes Videos

Change log (v2.3_BETA_2):

Warning, still in a Beta release. Using 2.2 is recommended.

- Fixed Top-Down Conversion"

Source:  http://gbatemp.net/topic/315687-3ds-video-converter/page__p__4014698#entry4014698