JM2-19 is an output. DDR Power will be generated with U3 see schematics page 15.
Do you mean it doesn't need to connect with the Pin from TEBA0841-02 baseboard. (See attached)
When does this message appears with JTAG ACK appears? During programming? Yes, when I run the elf file. (Bitstream is OK)
Which JTAG programmer did you use? How did you connect the programmer?
TE0790-03 -- DIP: On, Off, Off, Off
Why is you DIP S1-1 from the TEBA0841 carrier on on your picture? This should be off (I think it was off as you has see SoC in Vivado?)
I tested again with TEBA0841 carrier DIP S1-1 Off and it works. I changed the TE0790-03 JTAG programmer -- Looks like the other one is malfunctioning.
It seems my observation is wrong ... Sorry
Which external power supply did you use, where did you connect the 3.3V power supply? Some current limit?
I used 3.3V power supply-- I limit the curren to 1A.
You Vivado screenshot shows that PL is programmed. Design was load from QSPI?
Yes. It was one of my trials and you are right it almost with TEBA0841 carrier DIP S1-1 Off.
PS:
https://forum.trenz-electronic.de/index.php/topic,1313.msg6259.html#msg6259
--> here it sound like TE0715 was working but not TE0720 and TE0741 on the same TEBA0841. Do you use the same TEBA0841?For bitstraem programming there is no problem using TE0715-30 with baseboard TEBA0841-02.
The issue appeared when I tried to run the *.elf file from the SDK.
Thanks for your clarification... 
Regards,
Hossam