Although not a fix by no means I have used a workaround by modifying 
/etc/lirc/hardware.conf and changing the line from
REMOTE_LIRCD_ARGS="-d /dev/ttyUSB0"
to
REMOTE_LIRCD_ARGS="-d /dev/ttyUSB*"

If you have more than one ttyUSB device this will not work but I have
not had this issue.

-- 
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Bug Team, which is subscribed to lirc in Ubuntu.
https://bugs.launchpad.net/bugs/359356

Title:
  USB device attached to different ttyUSB after resume from suspend to
  RAM

Status in “lirc” package in Ubuntu:
  Confirmed

Bug description:
  Update: As for Xubuntu 11.04 at least, please read comment #13

  OS: 8.10

  USB device is attached to /dev/ttyUSB0 when I plug it in USB port. But
  when I suspend to RAM and resume, it gets attached to /dev/ttyUSB1.
  Consequently, the daemon configured using /dev/ttyUSB0 does not work
  after resume. I would expect the device to be attached to the same
  ttyUSB before and after.

  Details of the device (from output of lsusb -v):

  Bus 003 Device 010: ID 0403:6001 Future Technology Devices International, Ltd 
FT232 USB-Serial (UART) IC
  Device Descriptor:
    bLength                18
    bDescriptorType         1
    bcdUSB               2.00
    bDeviceClass            0 (Defined at Interface level)
    bDeviceSubClass         0
    bDeviceProtocol         0
    bMaxPacketSize0         8
    idVendor           0x0403 Future Technology Devices International, Ltd
    idProduct          0x6001 FT232 USB-Serial (UART) IC
    bcdDevice            6.00
    iManufacturer           1 FTDI
    iProduct                2 FT232R USB UART
    iSerial                 3 A5001qxI
    bNumConfigurations      1
    Configuration Descriptor:
      bLength                 9
      bDescriptorType         2
      wTotalLength           32
      bNumInterfaces          1
      bConfigurationValue     1
      iConfiguration          0
      bmAttributes         0xa0
        (Bus Powered)
        Remote Wakeup
      MaxPower               90mA
      Interface Descriptor:
        bLength                 9
        bDescriptorType         4
        bInterfaceNumber        0
        bAlternateSetting       0
        bNumEndpoints           2
        bInterfaceClass       255 Vendor Specific Class
        bInterfaceSubClass    255 Vendor Specific Subclass
        bInterfaceProtocol    255 Vendor Specific Protocol
        iInterface              2 FT232R USB UART
        Endpoint Descriptor:
          bLength                 7
          bDescriptorType         5
          bEndpointAddress     0x81  EP 1 IN
          bmAttributes            2
            Transfer Type            Bulk
            Synch Type               None
            Usage Type               Data
          wMaxPacketSize     0x0040  1x 64 bytes
          bInterval               0
        Endpoint Descriptor:
          bLength                 7
          bDescriptorType         5
          bEndpointAddress     0x02  EP 2 OUT
          bmAttributes            2
            Transfer Type            Bulk
            Synch Type               None
            Usage Type               Data
          wMaxPacketSize     0x0040  1x 64 bytes
          bInterval               0
  Device Status:     0x0000
    (Bus Powered)

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