I don't know about cubase so I can't help. About the gembench thing. It seems to me that your falcon is running at 8 Mhz and not 16. Unless of course you have another reference. I' d advise you to download the sysinfo utility and see if anything strange is going on. If it isn't much trouble please post the exact report of gembench.
Other than that there is nothing else I can thing off.
PS FPU is not standard in the falcon and the blitter might have been turned off.