Ok, better solution.... This is what will be in the new package, it's not pretty but it works.
1. FTP the e:boot.cfg to your PC.
2. Edit the boot.cfg, remove the # before the AltRomfile entry.
3. Save the file.
4. FTP it back to the box, overwriting the one in e:
5. FTP the xboxrom.bin from the gamesave dir to your PC. (Not the one in Audio!)
6. Rename xboxrom.bin on your PC to xboxrom2.bin.
7. FTP xboxrom2.bin to e:.
To boot and be able to see the CDRom drive in FTP:
Boot the audio hack up till it asks you to set the name for the new soundtrack. When you press A the xbox will load Phoenix. As soon as you hit A, eject the DVD drive. You must be fairly quick about this, but I was able to get it first try every time.
This causes Phoenix to load the AltRomFile instead of the normal one. This one does NOT load the dashstub (the source of the issue).
After doing this, put in the DVD you want to rip. You may have to refresh D: in your FTP client a couple of times.
The dashstub is kind of important, so I am hesitant to remove it completely, but this will give you an option of loading it or not.
Also, this issue doesn't seem to effect you if you are using an app native to the XBox to rip the DVD, only if you use FTP. (This is why I didn't see it in my testing, I was using XCommander.)
One more bug shot dead.....
Morden.
Edit - The bug dodged the bullet! I'll have to use a shotgun next time. This works, sometimes, you might do it ten times in a row with no problems, then ten times with. I found another work around but want to test the hell out of it before I mention it as I've been burned twice by my fixes in just the last few hours!!!!!