I don't know the precise answer to your query, but have you thought of using this instead:http://www.videohelp.com/tools/WinFF
Available in repos and so easy even I could use it, it is just a gui frontend for ffmpeg so it takes the guesswork and head scratching out of using the cli. (The site I linked to has other alternatives listed as well if you don't like that one).
Edit. Here is another one you might try:http://www.howtogeek.com/63011/how-to-c ... ntu-linux/
Haven't heard of that before, but just saw an article about it. I don't see a way to change the output folder in this case though.
Fujitsu Lifebook AH532 Laptop. Intel i5 processor, 6Gb ram, Intel HD3000 graphics, Intel Audio/wifi. Realtek RTL8111/8168B Ethernet.Ubuntu12.10 (Unity), Mint14 (Cinnamon), Manjaro (Xfce).