Same Problem.

I use VMWARE player and it can take control of USB devices. If I insert any pendrive Windows 2003 through VMWARE recognizes it as a USB 1.1 device. If I try the same trick booting my PC from windows the pendrive is recognized as USB 2.0 both by the host windows XP and the vmware windows 2003.

$uname -a
Linux ubuntu-best 2.6.31-20-generic-pae #58-Ubuntu SMP Fri Mar 12 06:25:51 UTC 2010 i686 GNU/Linux

$lsusb

Bus 006 Device 002: ID 046d:c521 Logitech, Inc. MX620 Laser Cordless Mouse
Bus 006 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 005 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 007 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 002 Device 004: ID 0781:5406 SanDisk Corp. Cruzer Micro 1/2/4GB Flash Drive
Bus 002 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 008 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 001 Device 002: ID 04f2:b064 Chicony Electronics Co., Ltd 
Bus 001 Device 001: ID 1d6b:0002 Linux Foundation 2.0 root hub
Bus 003 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub
Bus 004 Device 002: ID 08ff:1600 AuthenTec, Inc. AES1600
Bus 004 Device 001: ID 1d6b:0001 Linux Foundation 1.1 root hub

$ lsusb -vv -s 002:004

Bus 002 Device 004: ID 0781:5406 SanDisk Corp. Cruzer Micro 1/2/4GB Flash Drive
Device Descriptor:
  bLength                18
  bDescriptorType         1
  bcdUSB               2.00
  bDeviceClass            0 (Defined at Interface level)
  bDeviceSubClass         0 
  bDeviceProtocol         0 
  bMaxPacketSize0        64
  idVendor           0x0781 SanDisk Corp.
  idProduct          0x5406 Cruzer Micro 1/2/4GB Flash Drive
  bcdDevice            2.00
  iManufacturer           1 
  iProduct                2 
  iSerial                 3 
  bNumConfigurations      1
  Configuration Descriptor:
    bLength                 9
    bDescriptorType         2
    wTotalLength           32
    bNumInterfaces          1
    bConfigurationValue     1
    iConfiguration          0 
    bmAttributes         0x80
      (Bus Powered)
    MaxPower              200mA
    Interface Descriptor:
      bLength                 9
      bDescriptorType         4
      bInterfaceNumber        0
      bAlternateSetting       0
      bNumEndpoints           2
      bInterfaceClass         8 Mass Storage
      bInterfaceSubClass      6 SCSI
      bInterfaceProtocol     80 Bulk (Zip)
      iInterface              0 
      Endpoint Descriptor:
        bLength                 7
        bDescriptorType         5
        bEndpointAddress     0x81  EP 1 IN
        bmAttributes            2
          Transfer Type            Bulk
          Synch Type               None
          Usage Type               Data
        wMaxPacketSize     0x0200  1x 512 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     0x0200  1x 512 bytes
        bInterval               0
can't get device qualifier: Operation not permitted
can't get debug descriptor: Operation not permitted
cannot read device status, Operation not permitted (1)