I have same problem with my ElementaryOS 0.4.1 based on Ubuntu 16.04.
Kernel - 4.4.0-97-generic #120-Ubuntu SMP Tue Sep 19 17:28:18 UTC 2017
CPU - i5-3210M

I upgaded bluetoothctl from 5.37 to 5.46, but problem still exists.

$ dmesg | grep -i blue
[    3.113911] usb 1-1.2: Product: Bluetooth USB Host Controller
[    5.291238] Bluetooth: Core ver 2.21
[    5.292778] Bluetooth: HCI device and connection manager initialized
[    5.292783] Bluetooth: HCI socket layer initialized
[    5.292786] Bluetooth: L2CAP socket layer initialized
[    5.292793] Bluetooth: SCO socket layer initialized
[    5.379880] Bluetooth: BNEP (Ethernet Emulation) ver 1.3
[    5.379883] Bluetooth: BNEP filters: protocol multicast
[    5.379887] Bluetooth: BNEP socket layer initialized
[    7.407838] Bluetooth: hci0 command 0x0c13 tx timeout
[    9.411812] Bluetooth: hci0 command 0x0c52 tx timeout
[   11.796839] Bluetooth: RFCOMM TTY layer initialized
[   11.796846] Bluetooth: RFCOMM socket layer initialized
[   11.796851] Bluetooth: RFCOMM ver 1.11

$ lspci -knn | grep Net -A2; lsusb
02:00.0 Network controller [0280]: Qualcomm Atheros AR9485 Wireless Network 
Adapter [168c:0032] (rev 01)
        Subsystem: Samsung Electronics Co Ltd AR9485 Wireless Network Adapter 
[144d:4105]
        Kernel driver in use: ath9k
        Kernel modules: ath9k, wl
Bus 002 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 001 Device 005: ID 2232:1029 Silicon Motion WebCam SC-13HDL11939N
Bus 001 Device 004: ID 0cf3:3004 Atheros Communications, Inc. AR3012 Bluetooth 
4.0
Bus 001 Device 003: ID 0bda:0129 Realtek Semiconductor Corp. RTS5129 Card 
Reader Controller
Bus 001 Device 002: ID 8087:0024 Intel Corp. Integrated Rate Matching Hub
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 004 Device 001: ID 1d6b:0003 Linux Foundation 3.0 root hub
Bus 003 Device 002: ID 0458:6001 KYE Systems Corp. (Mouse Systems) GF3000F 
Ethernet Adapter
Bus 003 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub


$ dmesg | grep ath3k; dkms status
[    5.295230] usbcore: registered new interface driver ath3k
bcmwl, 6.30.223.271+bdcom, 4.4.0-96-generic, x86_64: installed
bcmwl, 6.30.223.271+bdcom, 4.4.0-97-generic, x86_64: installed
$ dmesg | grep ath9k; dkms status
bcmwl, 6.30.223.271+bdcom, 4.4.0-96-generic, x86_64: installed
bcmwl, 6.30.223.271+bdcom, 4.4.0-97-generic, x86_64: installed

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https://bugs.launchpad.net/bugs/1617619

Title:
  Problem with Bluetooth USB Host Controller: Connection time-out after
  connecting to device

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