I've come across here while I was trying to find a solution for the very same issue of myself. For my instance, it was also hardware issue.
Although all the schematic and design were looking identical to my eval board, my custom board was failing after each JTAG debug attempt and the debug stops. But, the application was uploading alright. Only the debug was problematic. Until I cycle the power it was staying stuck.
Finally I found the issue. It was about two function pins on the LAN8720.
According to the document "LAN8720A QFN Rev D Schematic Checklist.pdf";
The polarity of LEDs on those pins must be correct: LED2/nINTSEL and LED1/REGOFF
The LED functionality signal pins are shared with the REGOFF & nINTSEL functionality
of the LAN8720. The pinouts are as follows:
LED1 is shared with REGOFF on pin 3.
LED2 is shared with nINTSEL on pin 2.
My LED polarities were opposite to what they have to be. Once I corrected them, things started to act normal.