You mention that you have re-installed Windows in an attempt to fix this problem. I will assume that you have a set of CAB files available on your harddisk.
The first thing I would look for is a "noide" entry in the REGISTRY. If you find one, remove it and re-boot your system, and the Secondary channel should begin working again and your CD-ROM will be working. If you do not find this entry, try this:
Go to the Device Manager and open the "Hard disk controllers" section. Highlight the controller entry (not the Primary or Secondary, but the parent device). Click Properties, then select the Driver tab. Click on Update Driver and let the system Display a list of all drivers so you can select the driver you want. Select theStandard driver if you currently have the bus-mastering driver installed (or select the bus-mastering driver if you currently have the standard driver installed.) The driver you selected should load from the CAB files on your harddisk. Let the system re-boot, and see if the Primary and Secondary controllers are now working. If not repeat the procedure to re-load the initial driver. Sometimes, this re-loading action gets the drivers working again. Good luck.