need specifics of how video uploads are handled to diagnose an issue
Installation and Configuration
I don't know anything about cloudflair system sorry.
Once the file is fully uploaded 100% to the temp directory then the file is moved into the /media/ directory and given its correct name.
If its failing at the copy point then look for the issue in the destination directory, maybe limit on diskspace, or permissions. For whatever reason the newly uploaded file cant be moved to where it needs to go.
Take a look at the jrAudio module to see the save flow from a form, maybe check out
view_jrAudio_create_save() to see how its done in a form.
During the form submit save process the function jrCore_save_all_media_files() fires. That saves the file to the /data/ directory in a format like:
/core/data/cache/jrCore/12046f3177d5079e5528aa7a34175c73/1_audio_file
/core/data/cache/jrCore/12046f3177d5079e5528aa7a34175c73/1_audio_file.tmp
The that file then retrieved with jrCore_get_uploaded_media_files() function if you want it.
Another function to look at is jrCore_save_media_file() which processes the individual files.
Sounds like what your attempting to do is pretty advanced, it would be easier if you setup a debugger.
http://www.jamroom.net/the-jamroom-network/documentation/development/129/setting-up-a-debugging-environment