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By default, FS-UAE is set up to emulate the real Amigas as closely as possible (as realistic as the current emulation permits). For 68000-based models, this should be as good as the real thing. For 688ec)020-based ones, the (CPU) emulation isn't 100% accurate.
It could be something simple though, for example different kickstart version. In FS-UAE 2.5.33dev you can try the new A1200/3.0 model, perhaps that is more close to your real Amiga.
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