I have a problem with usb ports on udoo. Keyboards and mices connected to udoo via usb cables or usb radio dingles work fine. I was able to install debian 9 strech via usb sticks a few times despite some trouble - had to remount the install media a few times. It was a small net install image - about 200M. I was unable to install windows 10 via usb stick. The install program gave various error mesages ('A media driver your computer needs is missing.' or 'Windows can not find the Microsoft Software License Terms.) which i gather mean the install image was incomplete or rather could not be properly read from the installation media. I created windows 10 install usb stick multiple times using that Microsoft Tool. When in windows 10 system on udoo - hard disks connected via usb mount and umount repeatedly and that makes them unusable. When in debian - you can not mount them. The same hard disks connected via sata port work fine on udoo. The same hard disks (connected via usb) and usb sticks work on other machines (debian and windows 10). For testing I have used two hard disks (usb 3 and 2), two usb cables and 4 usb sticks. To conclude: Sata, M2 SSD, micro SD work fine. USBs work with keybords and mices and also sometimes - for short time - with usb sticks. USBs generally do not work with hard disk connected via usb and usb sticks. Its the same issue with all three usb ports. Is there some kind of setting - that i am not aware of - that could solve the problem? Other than that i am starting to think the board's usbs are somehow broken.
Are those hard drives powered via USB or with external power source? Many USB-powered hard drives are designed incorrectly on purpose and take more power from USB than what is allowed - so they might work on some computers or not. (I never buy any USB-powered hard drives for this reason.)
There are some reports that in this case in Windows USB power suspend has to be disabled: https://www.tenforums.com/tutorials/73187-turn-off-usb-selective-suspend-windows-10-a.html You could give it a try....
After updating board's firmware (https://www.udoo.org/docs-x86/Advanced_Topics/UEFI_update.html), usb ports seem to work fine.