I think it is a weird interaction between the transmutation table and ender IO. now I have one question, does the tier 1 capacitor hold 25M now?
Since I changed back the configs everything is normal. But for the sake of testing things I went to switch them back and noticed other key config options:
# The maximum storage for a single tier one capacitor in RF
I:capacitorBankTierOneMaxStorageRF=1000000
# The maximum storage for a single tier two capacitor in RF
I:capacitorBankTierTwoMaxStorageRF=5000000
# The maximum storage for a single tier three capacitor in RF
I:capacitorBankTierThreeMaxStorageRF=25000000
They were separate options from the one I changed in the first place. So I'm not 100% sure why the other option is really even there.
Ah, I know why it's there, it adjusts the depreciated capacitor bank that can't be crafted anymore. As to why the vibrant ones got stuck to 5,000,000 I think you're right with a "quirk" with the transmutation tablet.