Brewgo

Same here, got a clean install yesterday caused by some old mods incompatibility, installed something like 70 mods and started a new game, it was ok. Today I added a bunch of mods and started a new game again and I got lvl3 R&D at start. Last mods were: kerbin side Gap Unkerballed starts Firespitter core Firespitter resource config Airplane plus Custom barn kit. I think one of them is the problem and if I have to point my finger on one of them I would guess on custom barn kit. Anyway I just found a tweak. Ctrl+right click R&D, there will pop up an option to demolish it, do that, than ctrl+rightclick again and rebuild lvl2. Repeat to lvl 1 and you'll be done.