Do you have some more details? (You should not expect that generating a font and then importing it will produce you exactly the same VFB with which you started. Some things will change because of different data structures, especially when it comes to AFDKO-syntax features and FLS5-syntax classes.)
Has anyone experienced FontLab generating a font where the kern classes differ from the source VFB? I'm completely stumped as to why this is happening or how to get around it. I suppose I could use TTX or FontForge to replace the kern classes but I can't help wondering if this is a known bug, maybe FL needs a reinstall or perhaps I've overlooked something. Any insight would be appreciated.

