When I read the Oghma Infinium I gain 7 (strangely) perk points but gain no skill levels. I have repeated this with all of the paths, have tried dropping and picking it up, and have talked to Hermaeus Mora before reading it always. I play on PC but have no game-changing mods that should affect it.

Does anyone know how to fix this? Thanks

Try reloading a save?

Tried that :/ I went back to before I returned to Septimus then gave him the Extractor again etc., the book still didn't work.

See the http://www.uesp.net/wiki/Skyrim:Oghma_Infinium section, more specifically increasing the progress a little of the skills you desire to increase with the Oghma Infinium.