i dont know if this a bug or a mod conflict and i cant really explain it all that well
i've put it in a video
https://youtu.be/Xs79FGpK4uw

i did as instructed, and its more or less the same
both batteries is in the dual mode (input and output)
and everytime i leave the chunk it gets doubled
i recorded it again this time placing blocks before leaving
https://youtu.be/uGeUDJ9Z67A (sorry if its a long video)

Could you try placing a block in the same chunk as the battery before leaving? I believe it could be an issue where the chunk doesn't count as "modified" and is therefore not saved when unloading. Things like block placement will guarantee that the chunk gets saved.