I thought of checking BIOS settings, but given that both rear and front ports are using the same chipset and driver, that wouldn't make any difference. The only BIOS settings for USB are for USB Legacy support, USB 3.0 Legacy support, and EHCI hand-off, and I don't think any of that is related.
The only kernel parameter I've tried is iommu=soft and somewhere I found a suggestion for pci=nomsi but I haven't tested it.
Another possibility I found is that there's been a change in the kernel driver in the past that perhaps fixed a (not necessarily related) bug which caused this one. It may of happened sometime between Wheezy and Jessie, and has affected (apparently) other distros such as Ubuntu and Linux Mint. I have a spare hard drive, so I will try installing Wheezy and the Jessie and report the results.
uname -a
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Linux debian 4.9.0-3-amd64 #1 SMP Debian 4.9.30-2 (2017-06-12) x86_64 GNU/Linux
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00:1a.0 USB controller: Intel Corporation 6 Series/C200 Series Chipset Family USB Enhanced Host Controller #2 (rev 05)
Subsystem: ASUSTeK Computer Inc. P8 series motherboard
Kernel driver in use: ehci-pci
Kernel modules: ehci_pci
00:1d.0 USB controller: Intel Corporation 6 Series/C200 Series Chipset Family USB Enhanced Host Controller #1 (rev 05)
Subsystem: ASUSTeK Computer Inc. P8 series motherboard
Kernel driver in use: ehci-pci
Kernel modules: ehci_pci
04:00.0 USB controller: NEC Corporation uPD720200 USB 3.0 Host Controller (rev 04)
Subsystem: ASUSTeK Computer Inc. P8P67 Deluxe Motherboard
Kernel driver in use: xhci_hcd
Kernel modules: xhci_pci
06:00.0 USB controller: NEC Corporation uPD720200 USB 3.0 Host Controller (rev 04)
Subsystem: ASUSTeK Computer Inc. P8P67 Deluxe Motherboard
Kernel driver in use: xhci_hcd
Kernel modules: xhci_pci
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/: Bus 06.Port 1: Dev 1, Class=root_hub, Driver=ehci-pci/2p, 480M
|__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/8p, 480M
|__ Port 1: Dev 8, If 4, Class=Vendor Specific Class, Driver=qmi_wwan, 480M
|__ Port 1: Dev 8, If 2, Class=Mass Storage, Driver=usb-storage, 480M
|__ Port 1: Dev 8, If 0, Class=Vendor Specific Class, Driver=option, 480M
|__ Port 1: Dev 8, If 3, Class=Vendor Specific Class, Driver=option, 480M
|__ Port 1: Dev 8, If 1, Class=Vendor Specific Class, Driver=option, 480M
|__ Port 7: Dev 4, If 0, Class=Wireless, Driver=btusb, 12M
|__ Port 7: Dev 4, If 1, Class=Wireless, Driver=btusb, 12M
|__ Port 8: Dev 5, If 0, Class=Hub, Driver=hub/3p, 480M
|__ Port 3: Dev 7, If 0, Class=Human Interface Device, Driver=usbhid, 1.5M
|__ Port 3: Dev 7, If 1, Class=Human Interface Device, Driver=usbhid, 1.5M
|__ Port 2: Dev 6, If 0, Class=Human Interface Device, Driver=usbhid, 1.5M
/: Bus 05.Port 1: Dev 1, Class=root_hub, Driver=ehci-pci/2p, 480M
|__ Port 1: Dev 2, If 0, Class=Hub, Driver=hub/6p, 480M
/: Bus 04.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 5000M
/: Bus 03.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 480M
/: Bus 02.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 5000M
/: Bus 01.Port 1: Dev 1, Class=root_hub, Driver=xhci_hcd/2p, 480M
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[ 1.459390] ACPI: bus type USB registered
[ 1.459429] usbcore: registered new interface driver usbfs
[ 1.459442] usbcore: registered new interface driver hub
[ 1.459474] usbcore: registered new device driver usb
[ 1.460046] ehci_hcd: USB 2.0 'Enhanced' Host Controller (EHCI) Driver
[ 1.461526] xhci_hcd 0000:04:00.0: new USB bus registered, assigned bus number 1
[ 1.461952] usb usb1: New USB device found, idVendor=1d6b, idProduct=0002
[ 1.461954] usb usb1: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[ 1.461955] usb usb1: Product: xHCI Host Controller
[ 1.461957] usb usb1: Manufacturer: Linux 4.9.0-3-amd64 xhci-hcd
[ 1.461958] usb usb1: SerialNumber: 0000:04:00.0
[ 1.462122] hub 1-0:1.0: USB hub found
[ 1.462268] xhci_hcd 0000:04:00.0: new USB bus registered, assigned bus number 2
[ 1.465573] usb usb2: We don't know the algorithms for LPM for this host, disabling LPM.
[ 1.465601] usb usb2: New USB device found, idVendor=1d6b, idProduct=0003
[ 1.465603] usb usb2: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[ 1.465605] usb usb2: Product: xHCI Host Controller
[ 1.465606] usb usb2: Manufacturer: Linux 4.9.0-3-amd64 xhci-hcd
[ 1.465608] usb usb2: SerialNumber: 0000:04:00.0
[ 1.465775] hub 2-0:1.0: USB hub found
[ 1.465995] xhci_hcd 0000:06:00.0: new USB bus registered, assigned bus number 3
[ 1.466425] usb usb3: New USB device found, idVendor=1d6b, idProduct=0002
[ 1.466427] usb usb3: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[ 1.466429] usb usb3: Product: xHCI Host Controller
[ 1.466430] usb usb3: Manufacturer: Linux 4.9.0-3-amd64 xhci-hcd
[ 1.466432] usb usb3: SerialNumber: 0000:06:00.0
[ 1.466575] hub 3-0:1.0: USB hub found
[ 1.466715] xhci_hcd 0000:06:00.0: new USB bus registered, assigned bus number 4
[ 1.469583] usb usb4: We don't know the algorithms for LPM for this host, disabling LPM.
[ 1.469604] usb usb4: New USB device found, idVendor=1d6b, idProduct=0003
[ 1.469605] usb usb4: New USB device strings: Mfr=3, Product=2, SerialNumber=1
[ 1.469607] usb usb4: Product: xHCI Host Controller
[ 1.469608] usb usb4: Manufacturer: Linux 4.9.0-3-amd64 xhci-hcd
[ 1.469609] usb usb4: SerialNumber: 0000:06:00.0