Top most setup does not run.

The other two variants work fine.

All electrolyzers have energy.

Here is a MultiMC instance of the setup.
Nuclearcraft-Test.zip

I also found another bug. If inf water source block touches a reactor port, it will drain the reactor of RF.

All electrolyzers have energy.

Including the top one? So although it has energy, is doesn't run? If so, the issue is with the Electrolyser, not the Fission Controller, and given that the others are running fine, that would be very puzzling...

Yes, all electrolyzers in picture have energy.

I've only checked IC2 cables. Problem only shows up when cabling directly to the fission controller...As you can see the bottom setup is cabling directly to an RTG and yet works...very odd.

Could I have a screenshot of the GUI of the broken Electrolyser?

Melter seems similarly afflicted if connected to reactor through IC2 cable.

There seems to be a solution, which may also point you to the problem. If I add and remove a stack of speed upgrade into the entity to quickly deplete the energy reserve, then often I can jump start it. It will then continues to work as long as the speed upgrade(s) did not increase consumption in RF/t beyond the equivalent EU/t input, which depends on the setup.

A) For reactor -> Ic2 cable -> Electrolyzer/Melter => consumption must not exceed (reactor output/4) RF/t, e.g. reactor output 1600 RF/t, then speed upgrade must not increase RF/t beyond 400 RF/t.

B) For reactor -> Ic2 cable -> Ic2 Battery -> Ic2 cable -> Electrolyzer/Melter => consumption must not exceed the (Ic2 battery rated output)*4 RF/t <= This setup is "working" as a user would have expected.

C) The RTG->IC2 cable->Electrolyzer/Melter => same as A

From observation though, this is not just a mere graphical glitch but something deeper within the mod's interface with other mods' energy cables. Since your mod does not provide a conversion block, I will take note of the current behavior and work around the issue. It's a bug in my opinion, but not really a serious one.

Also what goes into the empty slot next to the slot for the speed upgrades ?

Well, whether it was me updating forge or IC2, I can not recreate this bug - here is a pic of the two electrolysers running. When I release the update, hopefully the issue will disappear for you as well.

As for the additional slot: at some point I am gonna add more 'specific' upgrades like Thermal Expansion's augments. I was gonna do it a while back, hence why the slot has always been there, but never got round to it.

Sure, I'll look at the issue again when you push a release

2.9e released :)

Problem still there. I used the same test world that I provided you. Broke and replace the Electrolyzer. It does not work until I force deplete its internal energy reserves with a stack of speed upgrade...

Is there anything that I am missing here?

Aha! I have the reason... that was quite tricky to spot, and I'll have to fix it.
Basically, there is a simple logic to when the machines actually run (provided they have a valid recipe, of course). If the total energy of the operation is lower than the buffer of the machine, then it will run when there is at least enough energy for the operation. Otherwise, the machine will run when the buffer is full. Because of some dodgy rounding when converting between RF and EU, not at all helped by the fact IC2 uses doubles rather than integers, the energy level of the Electrolyser that was not running was stuck at just under the buffer max.

Here is a hotfix that seemed to work for me - if this works for you, then I'll include the fix in the next update.

Works for me....I hope the fix will also work for the melter... I assume it will as likely it shared some code with Electrolyzer?