I was able to reproduce this! I also found this post over on the COFH github that possibly explained this weird behaviour.
In my case, I compared the file sizes for the energy api folder in all my mods, and found only a couple even had copies. one of them was enderIO, but it didn't seem to be the problem. The other was a copy of this folder found in Universal Electricity, and it *was* different. Removing the energy folder alone did not fix it, but removing that file that was present *with* the energy folder did! After realizing the folder was then empty, I just went back and took out the entire 'cofh' directory in the universal electricity zip file and now everything is working.