I may have the same problem as Wiowt.
All the thermal nossels I have tried only seem to support liquid hydrogen and atmosphere as fuel.
They won't accept liquid fuel, oxidiser or most of anything else they used to support and which is mentioned in the wiki. Also, they support hydrogen peroxide but I can't find any fuel tanks for that.
The reactor doesn't seem to matter either. I have tried some of the antimatter reactors and the pebble bed reactor. They work great with an intake in atmo but there seem to be something wrong with what fuel the nossels will accept.