Handbrake - M4V / MP4 Files With Flash Streaming Server Over RTMP

We are attempting to transcode some video to a format suitable for our Flash Streaming Server. In the past we have used Adobe Media Encoder (AME) CS4, but we are working with *.VOB files this time, and AME CS4 does not support them. We are attempting to use Handbrake now, as it has great support for h.264 and MP4 files. Unfortunately while the files play wonderfully on our local machines, they do not stream from the Flash streaming server over RTMP. The files come out of Handbrake with a *.m4v extension. Our old files out of AME CS4 are *.MP4's with h.264 and AAC audio. I can see no differences in video or audio codecs which leads me to believe it may be a container format problem. We are attempting to use Handbrake because it does an excellent job of batch encoding files and produces good quality files.