Your Atari is equipped with a USB hardware extension? In this case, if you are launching your USB drivers from the AUTO folder, you should consider launching them as HDDRIVER modules instead. The USB drivers of the Lightning VME and Lighting ST are prepared for that. Note though, that unfortunately the USB storage driver has known bugs in its SCSI Driver and XHDI implementation.
Adding USB support with modules ensures the best possible integration. Modules are executed before HDDRIVER.SYS, so that HDDRIVER knows at boot time how to access USB devices, as if USB support was built-in. This is especially useful for USB mass storage or keyboard drivers. You can select the partition to load the AUTO folder and ACCs from with the USB keyboard, for instance.
HDDRUTIL's "Devices and Partitions" settings, write protection or GPT partition scheme support are also available for USB drives. Furthermore HDDRIVER's XHDI functionality automatically becomes available for any drive managed by a driver launched as a module.
HDDRIVER itself can only be booted from an interface supported by TOS, because the first stage of the boot process is managed by TOS.
The HDDRIVER modules page provides links and more details, for end users as well as for developers. Sample sources are available on GitHub.