Thanks for the replies.

I also looked at the levels using the analog channels. It is the same result.

Makes sense that it works if there is a 1 ms delay to read the pin though. The delay shown is only 0.1 ms.

I can use a different solution to my problem that works in both cases.

Hello, in the ESP Docs there is a Boot Mode Selection guide. This states that EN needs to be pulled low. Then the boot0 pin is pulled to select either bootloader mode or run mode. The ESP32 will enter the serial bootloader when GPIO0 is held low on reset. Otherwise it will run the program in flash. ...