I have seen this before with Adobe Media Encoder. I cannot open H.264 files generated by the Blu-ray presets in QuickTime, however other applications see them just fine. When I use the Blu-ray presets in Compressor the files are able to open just fine in QuickTime.
The workaround would be to export from AE as a QuickTime with the desired settings.
My software:
Pro Maintenance Tools - Tools to keep Final Cut Studio, Final Cut Pro X, Avid Media Composer and Adobe Premiere Pro running smoothly and fix problems when they arise
Pro Media Tools - Edit QuickTime chapters and metadata, detect gamma shifts, edit markers, watch renders and more
More tools...