on the subject of hard drive games, we have a few that we've been operating for 4 years ourselves, and they were in the "care" of a tech at their previous location that didn't know his ass from a hole in the ground (meaning all-original drives) and I haven't encountered any problems with them. I wouldn't entirely rule out a bad IDE cable however.
I can tell you from my Area 51 board that it was very finicky with voltage. your board should also have 2 indicator lights saying low voltage and high voltage I think. mine was adjusted accordingly and within a couple months started doing the blackouts. that's when I started getting very serious about cleaning my JAMMA edge connectors, and cleaning it alone reduced the amount of power loss to the board components very significantly.
I am also a huge proponent for metering your roms to ensure accurate checks of voltage getting to the components... metering at the power supply and JAMMA edge are huge no-no's.
I created this thread (
http://forums.arcade-museum.com/showthread.php?t=215552 ) specifically for accurately testing your boards.
I've never worked with a Duo board before, but based on picture I saw the roms look to be mounted on the daughterboard, so you will only have to check one of those for voltage, cause the additional potential power loss would be to that daughterboard, assuming they're interlocked together. there looks to be an additional harness too, I don't know if that carries power or not.
at any rate, ensure that your roms are getting at least 5.10V and you should be mint. be sure to clean your JAMMA edge with a pencil eraser first, do each contact up and down, then do the entire edge side to side for maximum effectiveness, being certain you wipe away the eraser fragments off the board.
that should solve the puzzle, sorry for the tl;dr but I like to explain why this is all necessary