I recently borrowed the Mitsui Transcorder
(bottom) from work to rip my entire DVD collection. I replaced the SCSI CD writer with a SATA DVDRW on a USB bridge, and attached a USB->RS232 cable to the robot's command port. (the transcorder came with a shoebox 486 as a controller.)
Hooked it up to a linux box and wrote a shell script that used DVDDecrypt and dumped the entire contents of the disk to a storage drive. Worked well.
From what you describe of the predecessor's work and your own experience, I think there's either something wrong with the optics on the drive in the carousel, you have scratched/dirty disks, or the firmware on the carousel needs updating (whether or not said update is available). Actually, it's probably some combination.
The concept of a "bad slot" doesn't exist with a disk carousel, outside of a physical obstruction or actual breakage. There's only the one drive for reading/writing. The carousel's (the turny part) only job is to move the needed disk to where the mechanics can load it in and out of the drive.
Unfortunately, using a completely integrated solution like that, it'll be hard to diagnose and fix. Especially if you aren't capturing any messages output by DBPA during the ripping process.
Ditch the carousel and replace it with a robotic arm-based loader using one or more off-the-shelf drives. My personal preference would be to grab one with support for operating systems other than Windows, or at least sufficient documentation that you wouldn't have to reverse engineer the communications protocol (like I did) to control the robot if you wanted to roll your own control software. But your needs may vary.
If you're going to consider buying new equipment, might I suggest something like Primera's Bravo SE duplicator
? I know you don't need the printer, but I don't know that I've seen a current robot-based duplicator solution for less, even without a printer.
Or troll ebay for duplicators, then email the mfr to ensure that they'll sell you software that'll work for controlling it before you buy. The two main names in disk duplicators for the last decade have been Primera and Rimage.