Multiple Unit Train Control by Robot256 doesn't accept the batteries as fuel, as it replaces the default locomotive with a duplicate of the locomotive with .mu added to the end. Im not sure if its something you can fix on your end or if its something MUTC needs to change.

I opted to whitelist each vehicle that should accept batteries. So that would be a change on my end.

With only the mods enabled the MUTC locomotives pick up the batteries as acceptable fuel just fine. This is probably a mod ordering issue with another mod. Do you play with Krastorio2 by any chance and have its fuel overhaul option enabled? That resets vehicle fuels and forces me to re-add them later - which might be too late for MUTC to see them.

Testing with K2 and SE it's as I suspected. I'll fix that for now.