In some cases, configs created by FS-UAE Launcher needs to be launched via it. If you post the config in question, I can check if I see anything there.
Actually, if you use the portable version, that might be the problem. At least in 2.4.x, FS-UAE itself does not understand the portable directories, only the launcher does and starts FS-UAE "portable". This was improved in version 2.5.28dev, where FS-UAE itself also detects the portable directory.
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