I'm sad to report it seems to be a driver problem
. If you go into control_panel->system->device_manager->Universal_serial_bus_controllers and "disable" the "usb_serial_converter" that is the FTDI device your arduino should function normally (mine seems to). This is a kludge. It seems like sometimes you might even have to hit the arduino reset button to get it running properly. You can "enable" the serial driver again to download new code.
I don't know if this is an FTDI issue or arduino software problem. I suspect the FTDI driver is polling continuously or something weird like that though because shutting down the arduino software doesn't seem to help.
I think this might only be a windows vista 64 bit problem. That is just a guess though