the issue appears to be that the sdcard is 'not ready' when the startup attempts to load the patch (because you are doing within msecs for the board starting)
the simple solution, is to change in gpioctrl the delayedpulse to ~1sec , then reupload the startup patch.
however, that's not clean, as it means all patch changes are delayed by 1sec, (when you next upload them , and they don't need to be.
so what you could do is, leave gpioctrl as is, but copy its contents into your startup patch, change this only to 1sec, and then when you upload the startup patch, remember to disable controller script temporarily, since it doesn't need this.
note: the reason these issue have not been seen before is usually, users do some event (send pgm change) so the changing of patch is not normally happening so quickly (sub second) after the board is powering up.
@johannes this might be worth investigating further for future release,
perhaps loadPatchIndex etc need to be delayed if the sdcard (or its caching) is not ready - unfortunately, I didn't have my SWD cable attached to same board as pots, so couldn't dig much deeper to see whats going on.
(note: its definitely something to do with initialisation time, given if you unplug and plug in quickly, it works, presumably as the sdcard initialises faster? cold vs warm start?)