Using 12.2_x86 with KDE3, and getting 100k/sec transferring (copying) files from my HDD over a USB2 port to a USB2 flash stick. The same file transfer in Mint14_x86 Cinnamon over the same port to the same device is about 6 mb/s, and in openSUSE 12.2_x86 with Cinamon DM gives the same 6mb/sec transfer. All are separate physical partitions, not VMs.
On the same PC using Windows 7_x64, over the same port to the same device, the write speed is also 6mb/s or more. Makes no difference to all of the results if the transfer originates from an ext4 or ntfs partition, or if the flash drive is formatted fat32 or ntfs, in both Windows and Linux. The files I tested are 600mb to 1.5 gig in size.
I was surprised about the transfer speed in KDE3, as I assumed all the USB functionality came from the kernel and not the desktop manager.