@User: What is probably happening is that the serial load of the GPIO configuration takes a time equal to the number of GPIO pads * the number of config bits (11 or 12) * 1 (maybe 2?) clock cycles. Since there is no command to start or stop the user project from the management region, the user project counter is running during this time, before the GPIOs are configured. That suggests that it would be a nice-to-have feature for the "reg_mprj_xfer" bit to be available to the user project as a reset, so that the user project can be made to wait on the GPIO configuration before starting. I'll consider that for the next shuttle run.

Any workaround for sending a signal to the user project area that the GPIOs are now configured and the counter can start?

Use one of the logic analyzer pins and assert it once the pins are configured