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Did each JTAG UART end with a different instance ID? I forget what the value is but it should be something like 0C006Exx where xx should be unique between your two JTAG UARTs. If they overlap Quartus II should have raised an error during compilation so just check to make sure they don't indeed overlap.
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Correct, I have two (different) IDs ending in 00 and two (different) IDs ending with 01. Funny thing is, I can download a new NIOS app onto the JTAG debug module of SOPC#2, I can also connect to the JTAG UART of SOPC#2 but it does not output my messages. SOPC#1 works fine.
Also, I did not find any error messages in Quartus regarding the JTAG UART.
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