I have many at least 50 PCB schematic Libs with at least 50 foot prints. I've never had any issues linking them up or using them in a PCB I've actually created and ordered.
For some reason I am unable to assign the footprint I have labled "MICROSD MODULE 0.1 HEADERS BUGGED" to any Schematic Lib. specifically I'm trying to assign it to "MicroSD Module 0.1" Headers". In order to get around this I literally just copied everything to a new footprint lib. When I named this library anything called "MICROSD MODULE 0.1" HEADERS XXXXX" where X was any other text, the footprint library got bugged. I finnally just copied everything (again..from "MICROSD MODULE 0.1 HEADERS BUGGED") to a footprint called "MICROSD CARD BREAKOUT" and was able to assign it to "MicroSD Module 0.1" Headers" without problems
I thought someone might want to take a look at this to see what went wrong. I'll keep it around for a few weeks.