Hi,
this sounds weird. The CLK0 pin normally outputs a clock to the SDRAM, on this board it is used as clock output for the SD-card. But after reset it is configured for EMC_CLK0 function.
The pin 45 of CLK0 is not close to the JTAG pins, so a connection between these pins could only be caused by an external shortcut. Maybe test with an ohm-meter for shortcust between CLK0 and other pins, especially the ones from JTAG.
Regards,
NXP Support Team