I have the same issue. I also need to add a delay after I generate a RESETN pulse. We have connected the LMK04616 EVAL board to an VC707 eval board. The power of both boards is up for a long time so the power supplies should be stable.
When I do the power-up sequence without issue a reset pulse it works fine. When I add a RESETN pulse just before the sequence it does not work. When I add a 100ms delay between the RESETN pulse and the start of the programming sequence it works fine.
I could not find this behaviour in the datasheet.