Upon further testing and investigation, my original observation is incorrect. It seems that the blocks are mostly working correctly. It does not seem to be an issue with a specific version either. When I setup a simple UIFlow sketch to "Restart after 10 seconds", the first time I run it it correctly restart after 10 seconds. It then seems that the IRQ register isn't set right because it won't restart again if I immediately run the code again. If I instead power of the Core2 and then power it back on with the button on the side it will then run the code correctly and restart the device. It does not seem to be a hardware issue as the example wake on rtc code in the M5Core2 arduino library works correctly every time.