While going back and forth between real hardware, I found VCC is tolerant of not clearing FIRQ/IRQ/NMI sources (e.g. forgetting to read GIME register 0xff93 to clear the interrupt). I had to break out the oscilloscope to figure out what was going on. :) Applications that are written correctly don't have a problem, of course, but it makes cross-developing code more challenging since code that works fine on the emulator locks up the real hardware.