I had a similar problem with UAE dunping me back to to the xmb. My problem was a duplicate of the cfg file in the UAE folder that the pkg created on the ps3 file system. Once I edited that version, and deleted the usb equivelent, UAE worked well. I've tried both 1.3 and 3.1 kickstart rom on my fat jap 500gb without a hitch.
Its a great project, even Octamed was usable. Hopefully hd support and maybe an increase in resoloution will be supported later. Workbench could be a nice easy alternative until linux is back.