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An interesting phenomenon indeed. Real-time ISP basically means, that the existing MAX II design is not halted during programming. Thus in your hardware design, something seem to affect MAX II programming, if the design is halted, sounds odd. It may be a power supply related problem or due to some special hardware connected to the MAX II. Not a common problem, I think.
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Thank you FvM. I think it is not a common problem too. I build another board, the same to the first one. The same problem occured. Quartus cannot programming the device. But "Autodect" can list the jtag chain contains only one EPM570 device.
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