Okay. I've switched to using a windows OS, and now I'm not having that specific problem anymore.
However, I have this problem instead:
I delete the energy files, and replace it with the ones from the zip. (I did change the prefix from EnergyNet$EnergyNet$ to EnergyNet$, in a attempt to get it to work, as the original IC2 files have this prefix)
I drag and drop the rocketscience.jar file into the mods folder.
(do I need to post the error report? I was using 7zip for this)