Studio 4 and ATMega128 UART1

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I have been working with the JTAG ICE and a Mega128 part trying to debug a serial protocol working on the UART1. For a while I was trying to do all the work with Studio 4 but I kept on getting bytes out of the UART that the Program was NOT sending. Finally I switched to Studio 3.54 only to see that this effect dissapears. Just to be sure again I restarted Studio 4 with a very simple program that the only thing that did, was to enable UART1 and its interrupts. Every time I instructed the ICE to single step I got bytes from the UART. With the press of F5 - GO instruction the program sent again a few bytes starting execution but then stopped. I did this test with Studio 3.54 only to see that I was right and that nothing was sent on the serial line. Just to be more complete I have to say that the UDRE interrupt was NOT enabled.
Although the description is small, I must say that a lot of hours have been spent until I got to finding what was going wrong. I guess that the JTAG interface instructs the device in sending these bytes without them being part of the project.

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