CHDK should not interfere with normal USB downloads, unless you have USB remote enabled. If you do have USB remote enabled, it will prevent them from working no matter what OS you use. It is extremely unlikely that CHDK interferes with connections from windows but not linux.
If you install the libusb driver to use the CHDK PTP extension, this will usually prevent normal windows software from accessing the camera. The exception to this is old cameras (probably ones that don't return a serial number) where the INF driver is specific to a physical USB port.