I met exactly the same problem as in the related thread.
And I find the problem happens when I power the board through the docking JP2.
If I power the controlcard through J200 port, the problem is gone and the JTAG could be connected.
In both cases I connect J1 on the controlcard for JTAG connection.
And in both cases, LD1 and LD4 are on.
Why can't I power the board through docking JP2?