What else might cause the processor to not responding or booting up? I have checked the clocks, voltages, and reset state. All are correct, but I get the following below.

[EDavi]

I have the stm32f417 connected through 10 pin JTAG connector to a Sagger J-link debugger. I am using the SWD pins only. My prototype was working without issue, but now it sometimes it works and sometimes it doesn't. I have two more prototypes performing the same way.

As I understand it, as long as you have the reset inactive, clocks, and power to the processor. You should be able to at least communicate with it by SWD lines.

Question what else might cause the processor to not work?

I have checked the clocks, voltages, and reset state. All are correct, but I get the following below.

Checking target voltage...

Target voltage: 3.33 V

Listening on TCP/IP port 2331

Connecting to target...ERROR: STM32: Connecting to CPU via connect under reset failed.

ERROR: Could not connect to target.

Target connection failed. GDBServer will be closed...Restoring target state and closing J-Link connection...

Could not connect to target.

Please check power, connection and settings.

Shutting down...

ERROR: STM32: Connecting to CPU via connect under reset failed.

[Tesla DeLorean]

Well "Connect under reset" implies you would have NRST connected, not just SWDIO/SWCLK

It takes time for the debugger to connect, figure several thousand cycles, if your code goes into low power mode, or reconfigures the pins/clocks you could break debug connectivity. Try with BOOT0 pulled HIGH, rather than LOW

Try using the J-LINK utilities directly