Совершенно случайно нашел информацию о том, почему происходил этот глюк.
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The Index Pulse (pin 8) is "Masked" by a Seek Complete signal. In other words the Index Pulse signal is off during a Seek. (So is the Read Data.) Some of the older models had a jumper to control this but current production drives have no jumpers. Current production drives that mask the Index Pulse during Seek operations will not work
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Информация взята вот отсюда: http://www.swtpc.com/mholley/35disk/Disk.htm