Чисто случайно нажал сюда. Читаем внимательно:
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4. MDOS3 and WD Caviar HDDs
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Harddisks made by Western Digital are creating their own standards,
but MDOS3 can operate with these. Bootloader was changed, so that HDD now after
turning on will receive INITIALIZE DEVICE PARAMETERS command as well as
after reseting HDD (every ZXS reset). If WD Caviar is connected as single device, without any slave, DON'T PLUG IN THE
JUMPER, because it will cause disks are waiting 30 seconds for slave device response.
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А теперь качаем прошивку, смотрим как именно сделано, и фиксим наш софт!