The FX3 JTAG port has internal pullups of 50k on all connections except TCK which has a 10k pulldown, according to the data sheet.
The FX3 devkit PCB has 10K pullup resistors on all these pins. Is the conflict on TCK intended? And if I want to use the same JTAG debug cable on my own board as on the devkit, is this arrangement what is required?
The pull up resistors on the FX3 DVK will be removed in the next revision. The statement that has been mentioned in the data sheet is correct. You don't need any external pull up resistors.