Unfortunately my X99 Sabertooth has the same issue (all the buses on the same controller) even after BIOS update :'(
lsusb Bus Device ID Device Name
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 002: ID 0a12:0001 Cambridge Silicon Radio, Ltd Bluetooth Dongle (HCI mode) 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 003: ID 05e3:0608 Genesys Logic, Inc. Hub 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 004: ID 8644:800b Intenso GmbG Micro Line (4GB) 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 005: ID 0c45:62e0 Microdia MSI Starcam Racer 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 006: ID 174c:2074 ASMedia Technology Inc. ASM1074 High-Speed hub 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 007: ID 056a:00d1 Wacom Co., Ltd Bamboo Pen & Touch (CTH-460-DE) 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 008: ID 046d:c517 Logitech, Inc. LX710 Cordless Desktop Laser 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 009: ID 10f5:0650 Turtle Beach 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 003 Device 011: ID 1e3d:2092 Chipsbank Microelectronics Co., Ltd 003 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub 004 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 004 Device 002: ID 05e3:0732 Genesys Logic, Inc. All-in-One Cardreader 004 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 004 Device 003: ID 174c:3074 ASMedia Technology Inc. ASM1074 SuperSpeed hub 004 00:14.0 USB controller: Intel Corporation C610/X99 series chipset USB xHCI Host Controller (rev 05)
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub 001 00:1a.0 USB controller: Intel Corporation C610/X99 series chipset USB Enhanced Host Controller #2 (rev 05)
Bus 001 Device 002: ID 8087:800a Intel Corp. 001 00:1a.0 USB controller: Intel Corporation C610/X99 series chipset USB Enhanced Host Controller #2 (rev 05)
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub 002 00:1d.0 USB controller: Intel Corporation C610/X99 series chipset USB Enhanced Host Controller #1 (rev 05)
Bus 002 Device 002: ID 8087:8002 Intel Corp. 002 00:1d.0 USB controller: Intel Corporation C610/X99 series chipset USB Enhanced Host Controller #1 (rev 05)
Bus 005 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub 005 08:00.0 USB controller: ASMedia Technology Inc. ASM1142 USB 3.1 Host Controller
Bus 006 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub 006 08:00.0 USB controller: ASMedia Technology Inc. ASM1142 USB 3.1 Host Controller