I think I recall that you have WinXP on the machine in question?

"Access is Denied" Error Message When You Try to Open a Folder (KB810811) may be some help with the folders that can't be accessed. The article describes a particular cause that doesn't look likely here; but gives a general procedure for "recovering ownership" of a file when your account privileges for one or more individual files are mangled. No guarantees here, but in theory it has a fair-to-good chance.

In older systems, you'd likely just go to a DOS window, but the Command Window inside WinXP recognizes accounts, and a "DOS boot" sometimes can't read (all of) an NTFS partition which you probably have. WinXP Pro includes a "Recovery Console" that might help; but it's a hairy mess to get into (and out of) so I'd avoid it except as a last resort.

It does sound like you may have a mixup with jumper settings, and if so that needs to be corrected to some consistent set of jumpers. Details vary somewhat with individual drive mfrs. Note that the connectors on the cable may be specific Master/Slave (for EIDE) and need to match the jumpers on the separate drives: Master connector to Drive with Master jumper, etc.

A normal procedure with drives that don't get recognized is to go to Device Manager (Start|Settings|Control Panel, Double Click "System," Hardware Tab, Device Manager button). If the DVD drives both show, simply delete the drivers for both of them and then reboot. PnP will find new drivers and should sort out drive labels and priorities for them. Default drivers from the system CAB files may be used, but if an updated driver has been installed, it usually gets saved to the CAB folders when you unload it (isn't just deleted) so that the new one often comes back re-installed; but once you get the drives recognized you can go back and do a driver update if needed. (A 2-year old DVD drive may also have a Drive BIOS update available, so check later when the other stuff is fixed.)

It probably would be a good idea to look in Control Panel Add/Remove Programs and see if any of the "specials" that you downloaded during this manipulation appear, indicating that an installation was attempted. Removal, and reinstallation after the hardware gets sorted out, would likely be a good idea just on principle, but you can use some degree of judgement on that.

John