Hmm, sounds like a weird bug indeed. Doesn't sound like you've done anything wrong, but Is it an option for your to tell FontExplorer NOT to manage the font files and just do it yourself? It sounds like you already have your files organized well.
I've more that 65MB of fonts in my FEX Library and haven't had any problems, even when the app was in beta, but I manage the files myself and just import them to the app.