1. Suggest setting USB ports not needed for BIOS or boot to "No Detect" under Devices/USB/USB Ports to minimize number of devices the BIOS must enumerate. Make sure you leave at least one port from 01 thru 04 enabled so you can still have keyboard support in the BIOS.
2. You could try attaching the USB3 drive via a cheap USB2 hub to force a USB2 connection. USB2 is way more reliable than USB3 across the board.
3. It could be an interoperability issue with your drives. I'm using a Silicon Power 64GB (SP064GBUF3B30V1K) with Phison controller. I haven't seen any issues, but I mostly boot from SATA.
4. You could add an mSATA drive to boot from. Better write endurance and more random iops than a USB stick.