Common FBA romset with RetroArch (Windows) with RetroPie?

I have a working RetroPie 4.0 system where I prefer to use FBA as it has more modern Capcom arcade games. I used 0.2.97.38; everything works fine. I was hoping to use the same romset on my windows 10 RetroArch installation. When I scan the folder containing my FBA roms, only a quarter of them show up. Is this a matter of core incompatibility and is there a way to use my existing roms without converting them with clrmamepro?

Sorry if this is simplistic question.