Are you by any chance using a USB hub?
I originally had a d-link powered USB hub in my arcade cab. When I had my ipac4 plugged into it, the computer refused to get past POST and wouldn't boot. I could also start the machine without the ipac4 connected, and plug it in once the machine got past POST, and all was well. I didn't like this solution, so I replaced the d-link hub with a kensington powered hub, and the problem went away. I'm not sure what the problem was, but the d-link hub and the ipac4 didn't get along during boot.
I had another *kind of* similar problem on my jukebox, but it doesn't actually prevent boot, it just delays it, for literally 15 mins. On my jukebox, I have the same kensington powered usb hub, but this time, if there are ANY storage devices plugged into it at boot (external USB drive, flash drive, whatever) it will literally take 15 mins to enumerate the drives before booting. This one was a simple fix, I moved the external storage devices to plug directly into the computer, and used the hub for mouse, keyboard, wifi and touchscreen connections.