Thanks, I managed the reproduce the problem, and I have investigated some. ROM handling code has changed in the latest WinUAE betas, and a side effect in FS-UAE is that parts of UAE don't think the Cyberstorm ROM is loaded / activated (simplified explanation).
I'm still determining the best way to fix it in FS-UAE, but you don't need to provide any more help / debug information
Until it is fixed, the problem can be worked around by using the accelerator_rom option, and point this to your cyberstormppc.rom file. FS-UAE Launcher does this automatically, which is why it "accidentally works" when launched from FS-UAE Launcher.