Its software (virtual) for mounting isos and stuff. Software wont change the jumpers!

To be honest last time that happened to me was when I used windows 98. I just booted off the startup floppy, then went back into windows and they were back.

Like Karanislove said, check device manager first. If there are yellow exclamation marks double click on them and somewhere will have the option to reinstall the drivers.
I reckon they wont be there though.