Sorry, i hit return early, while chaning my machine model, sigh.
Regardless, I tried to convert an MP4, which didn't work on my iphone to one that would work on my iphone. It took 3 days on another machine of mine, an iMac, which is over 100x longer than it normally takes me using handbreak.
When the file was finally done, it was correctly placed in my library, and it went on the phone fine. Trying it, however, i get "This movie format is not supported"
Now i'm a fan of itunes, but this is insane. Please take this out, and make it work before taking it out. I know you can't really use FFmpeg, and nothing seems to be near it's speed, but 3 days.