In the past 5 years, many changes have been made to the IDE interface. A number of settings CAN give you the results that you found. What you found is actually quite common because of timing differences of the interface.
The IDE interface is nothing more then a "bus" because the actual interface per say is located on the HDD. The place where you connect the cables on the system board/controller is nothing more then an adaptor to adapt to the system board bus to the IDE HDD/peripheral.
In those years, the following is very important:
1. The cables from the IDE device(s) in total can not exceed 18 inches per port/channel.
2. The system "bus clock" must not exceed 33mhz (PCI) or 8mhz (ISA). This is the I/O slot speed, not the CPU speed.
3. Only 2 devices per port/channel.
4. Some devices acted badly when slaved/mastered to another device, try shuffling the devices.
5. The IDE adaptor/controller is very suceptable to noise (electrical), keep cables short and away from metal if possible.
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