Hi
I use the mega128 and also serial comms but unless you program via jtag the one serial port is normally used for spi programming , and unless you want to plug and unplug to isolate the programmer or have some electronic switch the best is to use only the second channel for serial comms and if you need an extra serial channel mainly for debug output - create a software serial port .
Also make sure about all the power pins - can cause problems if floating .
Cheers
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