Can you try powering the screen from the cigarrette lighter or something, to see if it is a power problem.
It could be a wierd driver issue. I am not very familiar with the AOpen, but does it have more then one video output option. Perhaps once it boots into windows, it is switching the video output setting. Why it works the second time around, if NOT BOOTING INTO SAFE MODE, I can't figure out. Are you using powerstrip or any other program to try and manipulate the video output? Perhaps it is not starting that program the second time around. I have a feeling because it is booting into safe mode, but I guess we will have to see.
If everything is the same betweem a "bad" boot and a "good" boot, then it will be near impossible to figure out.