This auto upgraded when I restarted Factorio today and it completely broke my factory.

Firstly, all nuclear furnaces now require a recipe. I thought this was a bug but it seems deliberate. Normally they just take what's fed, but now you need to specify what to melt or they sit there doing nothing. Why?

Secondly, the throughput once the above is selected is dismal - hardly any faster than a steel furnace.

I've now downloaded v.1.1.1 again and all is good, so I don't think it's a conflict with another mod. (In fact, I removed all other mods and it still did this).

Looking more closely, the nuclear-furnace.lua file has been removed entirely from this package, so it's trying to use the extractor-inserter.lua as the furnace, which explains why it now needs a recipe and the throughput is capped to the speed of an inserter.

@NightOps

Seems more like you haven't read the changelog at all to see what changed. There are new options that can be turned off in the mod settings.

Noted - I had overlooked that. However, even going into Mods Setting (only available from base menu, not whilst in-game), the settings don't appear to make any difference to the described behavior.

The throughput limitation you see might be due to the limitation of recipes only being able to be made once per tic. Also, if tiered furnace is enabled, the first tier only starts out with a crafting speed of 7.5, not 140 which is the case without tiers. Each tier upgrade doubles crafting speed however. Still much better than even the electric furnace even starting out. If you want typical furnace like nuclear furnaces instead of having to choose the recipe, be sure to set the furnace type setting to "furnace", not "assembling-machine".