Ok, this will be a pain and You'll need SSH to make this happen.
In almost all kind of settings combination, I was not able to convert anyting at all.
So I wanted to go this way to see if this works.

/usr/bin/ffmpeg -i '/home/user/domains/mydomain.com/public_html/video/filetoConvert.wmv' -acodec mp3 -ar 22050 -ab 32 -f flv -b 1000000 /home/user/domains/mydomain.com/public_html/flvideo/videofolderName/videoName.flv

Yes, I am able to convert now. But, videoFoldername and videoName.flv must be obtained thru the panel first. This means, You'll try and fail, get the file and folder names that's written to db, and then convert.

But, since the code is not encripted, I'll try to apply this command to the .php script tomorrow and see what happens. Sorry for the delay but I am in a process of moving 2 sites and apply the database changes on them.