I ran the provided download.bat file. Everything seems right. In the command window, I saw both logic and software were downloaded successfully. But the software wasn't running since I had no output in the serial console (I verified all the settings were right), and the Chipscope didn't give me the right waveform I expected.
Then I commented the last four lines of download.tcl script (basically just initialize the PL and PS without downloading and running the software). After I downloaded the software from SDK, I saw the expected serial console output and this time the waveform in the Chipscope was also as expected.
Has any one run into this issue? Is this a Xilinx problem? Or is there something wrong with the TCL script?