System Workbench for STM32

Hello.

I've also encountered something similar to the above mentioned problem when running the debugger with a known-to-work application.

Eclipse Version: Neon.3 Release (4.6.3) Build id: 20170314-1500
Target Board: STM32L496ZGT6 Nucleo-144 demo board.

When trying to enter into debugging mode via F11 the console window reports the following:
STM32L496ZGTx.cpu: target state: halted
target halted due to debug-request, current mode: Thread
xPSR: 0x01000000 pc: 0x0800a034 msp: 0x20050000
STM32L496ZGTx.cpu: target state: halted
target halted due to debug-request, current mode: Thread
xPSR: 0x01000000 pc: 0x0800a034 msp: 0x20050000
STM32L496ZGTx.cpu: target state: halted
target halted due to breakpoint, current mode: Thread
xPSR: 0x21000000 pc: 0x20000068 msp: 0x20050000
Warn : keep_alive() was not invoked in the 1000ms timelimit. GDB alive packet not sent! (1845). Workaround: increase "set remotetimeout" in GDB
STM32L496ZGTx.cpu: target state: halted
target halted due to debug-request, current mode: Thread
xPSR: 0x01000000 pc: 0x0800a034 msp: 0x20050000

Note: the "Warn" statement above is new.
After pressing F8, the application is NOT behaving correctly. If would appear that the time bases are incorrect.

Ending the debug session by pressing +F2 results in a dialog box popping open that states:
Failed to execute MI command:
--stack-list-frames 0 0
Error message from debugger back end:
Invalid thread id: 1

Perhaps there is something in common here with the OP.