Ok, people - I am working very hard on .mp4 file authoring tool. This tool will include optimized AAC and MPEG-4 Video encoder.
At this state it is pretty unfinished, it encodes audio files only, but I suppose I will make it work with video, too - in a few weeks.
Another problem arise with .mp4 standard - there are not many tools with .mp4 I/O ability and the compatibility between them is not on a very high level. I rely on MPEG4IP reference implementation which is going to be ISMA 1.0 compatible.
I have whole bunch of various .mp4 files and implementations. Philips .mp4 works with Envivio (and won't work with Philips Webcine v1.1), but UBStream won't read them at all.
MPEG4IP would read some of Philips files, also it reads FhG IIS audio .mp4 files - Envivio and Philips won't read FhG audio files

ISO REFSOFT .mp4 library seems to work fine, but it is not documented (it is not in final state) - complete mess