CampbelltownDude
Great job of sorting through the details to get Premiere Elements 12 to work for you. Just in case note, if you have not updated 12 to 12.1 Update, please do so using an opened project's Help Menu/Update. The rest of the reply is an assortment of details for you to consider.
Details.
As for batch converting of files, you might want to explore MPEG Streamclip for that purpose.
http://www.bothell.washington.edu/it/howdoi/articles/mpegstreamclip
However, when you talk about converting your source to MPEG4, do you really mean going from AVCHD.mts ot AVCHD.mp4, that is, recording with the AVCHD video compression but with a .mp4 file extension or converting your AVCHD.mp4 to MPEG4 compression with a .mp4 file extension.
I am assuming by audio 6 channels, you are referring to Dolby Digital 5.1 channel (which is represented in properties as 6 channels).
What is the project preset that you (manually) or the project (automatically) has set for your 1080p60 source video. You can verify that information in Expert workspace Edit Menu/Project Settings/General. It should be
NTSC
AVCHD
AVCHD 1080p60 5.1 channel
but there is only
NTSC
AVCHD
AVCHD 1080p60
but you can create an AVCHD 1080p60 5.1 channel project preset for this project.
You could explore the use of a project preset with 5.1 channel in its description to determine if any of your issue was impacted by that factor.
At this point, I am not sure of the camera audio setting regarding built in and external microphones. It looks like you are always going to get 2 channel stereo
from the external microphone. And, the specifications that I looked at suggest either 5.1 or 2 channel for the built in microphones. You seem to suggest that whichever microphone, the resulting video file has 5.1 channel audio.
Best wishes moving forward with your Premiere Elements projects.
ATR