Here's a list of known issues with the current version of the simulator.
SD card slot is a little finnicky
If possible, use USB0. Performance testing has indicated that a USB drive in USB0 has performance exceeding that of the SD slot anyway, so this is the preferred storage port. If you have a Rev B2 board this has been corrected with a much easier to use slot.
Device is much lower power than an optical drive
Certain power supplies may expect a larger load on 5V or 12V lines, and so fail to start up correctly. In this case, you may need to install a load resistor over one or both of the power lines in your machine. Please ensure to use a resistor with a sufficiently large power capacity.