This issue occurs when you boot the ESXi host from a USB device or a SD card and the image is loaded to the memory which includes the esx.conf file. When you enable the USB controller for passthrough, all USB devices are invisible to the kernel. When you deselect the USB controllers from the passthrough list, the change saves to the esx.conf file. The esx.conf file is in the memory during ESXi uptime and when you issue the reboot command, the esx.conf is saved back to the USB device. In this case, the kernel cannot see any USB devices, so the configuration change does not get saved.

To avoid this issue, enable USB devices for passthrough instead of enabling a USB controller for passthrough.

Note: VMware does not support enabling USB controllers for passthrough if the ESXi host is booting from a USB device or SD card connected through the USB channel.

To work around this issue, burn a new ESXi image to the USB device or SD card.

Caution: All ESXi configurations are lost after re-imaging.

Alternatively, to work around this issue on a system with multiple USB ports, use a USB port on a different USB controller for booting, and never enable it for passthrough.