John
For what it is worth, I had a similar problem - SAMs fluttering, all SAMs on the backrail not functioning, and some SAMs always energized. Your statement "one full row is not working, and the other positions are random. i suspect a wire is loose for the row, but the random could be wire, or diode." I found a bad (intermittant) common connection between the stoprail SAMs and backrail SAMs. This condition would also damage the 74HC165N on the DIN board corresponding to the first SAM on the backrail every time a backrail SAM was activated (I changed a lot of I.C.s). I discovered this by careful visual inspection. I am using jOrgan under Windows XP, 3 MidiBox Core 8's, and latest DIN and DOUT boards.
Al