I solved the problem! For some reason spot loaders don't load the molecular transformer correctly and create the glitch. By using a world anchor from railcraft, I resolved my issue.
I believe I found a bug involving advanced solar panels. When I connect advanced solar panels and hybrid solar panels to a molecular transformer and unload the chunk, all of the machines disconnect to the wiring. The area is chunkloaded with chickenchunks spotloaders. The wiring I'm using is glass fibre cable. Thank you in adcanced.
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