yipes sorry bro i only use 3GP to do files for Ipod. Some files dont work i know that but it could be the video is corrupted or 3gp is messed up try configuring the setting again.
Everything was working fine before I used newer versions of ffmpeg (I used files that worked before as a test) so if I want to revert it, I just have to replace the files with the original content. The only reason I'm using a newer version is because of its increased file support. It didn't put the file into the folder I specified when I tried converting it. Instead, I checked the Temp folder to see if it's there, which it was. However, when I played it, there was no sound. The sound codec was aac and according to the newer versions, it uses libfaac (which I'm assuming there's a library for aac available to use instead of the external encoding information from Quicktime).
As for QT3GPPFlatten, I've no clue what that does specifically (I wouldn't mind if someone explained it to me) but I'm assuming the reason it's giving me the error is because ffmpeg seemed to have messed up the 3gp file in the end therefore preventing QT3GPPFlatten from reading it correctly.