MOV to MP4 conversion issue

I used to use Flash videos on my web site but am now in the process of changing them to improve cross browser compatibility.

I'm in the process of converting a number of MOV videos to MP4 for the purpose of posting them on the web site. It's been a frustrating experience and I've been going around in circles as noted in my other post:
http://forum.videohelp.com/threads/3...29#post2204429

My problem is finding the proper method of converting the MOV files to MP4.

I've used a number of programs including:
Xmedia Recode
Leawo Video Converter
Handbrake
WinX HD Video Converter Deluxe

All converted MP4 files play perfectly on VLC player but not all of them will play in all browsers when posted to the web (either in HTML5 or using JW PLayer or Flowplayer). I'm stumped because I can't find a common element that consistently causes the failure.

Usually the video fails to load in some browsers but is OK in others

The program MediaInfo reports the following info for some of the different converted files:
Writing App: DigiArty AV Encoder Core - AVC
Writing App: DigiArty AV Encoder Core - MPEG-4 Visual (Simple@L1)
Writing App: Handbrake - AVC (Baseline@L3.1)(2 Ref Frames)
Writing App: Handbrake - AVC (Baseline@L2.1)(2 Ref Frames)
Writing App: Lavf54.36.100 - AVC(High 4:2:2@L3.1)(2 Ref Frames)
Writing App: vlc 1.0.0 stream output - AVC(Main@L5.1)(CABAC/1 Ref Frame)
Most of them are 800x448 at 29.970fps
I have also varied the frame rates

I won't pretend to understand all of the above and there are many other options that can be set in some of the conversion programs like Xmedia Recode and Handbrake.

Can anyone point me to a reference that specifies the correct MP4 options for web posting?