Hi guys! I’ve managed to solve the problem. So just gonna down list the steps I did for future reference!!!
1. Bounce out 6 mono files from 5.1 Mix.
2. Send to Apple Compressor, format is Quicktime Surround (.mov)
3. Send to Final Cut Pro, Surround Project, Export Media as H.264 .mov
4. Send to Handbrake, export out as mkv, Constant Frame rate, Ac3 Passthru.
DONE!
Thanks guys for your help! Much appreciated.