So I may have figured out my problem, and it has nothing to do with iTunes. Well, not directly anyway. iTunes is still responsible for deleting the songs but I think the issue was caused by an incorrect time setting.
Background Info: I keep my media files on a network file server (device) made by NetGear. It's a simple home RAID disk cabinet. I have two of these devices, each with redundant disks. I have my iTunes configured so rip / save files to this device.
A bit over a month ago I purchased an upgraded unit. It had larger drives, but more importantly it was a faster CPU and had more memory, so the overall performance upgrade was very nice. That's where my iTunes library lives now.
On or about the same time I upgraded the system software for both units to the latest version.
All of this was done, and I never noticed any issues with iTunes. So I discounted that this might be part of the problem.
However, if you've been reading my (frequent) updates to this thread, you might remember that as a test I used iTunes 10.6 to rip a few discs to my wife's computer to see if I could recreate the problem. I could not, as everything worked. Yet on my computer it was still happening. In fact, the last test I ran involved ripping a single cd and them immediately syncing to my iPod. The entire CD was deleted from my library, yet every one of the songs got copied to my iPod.
Fast forward to this morning. I have a backup script that runs on the NetGear device at about 2:30 am, and I get an email from the script showing that the files were successfully copied. The files are stamped wtih the date and time of the backup. Now some time back (weeks ago) I started noticing that the backup times were off by one hour, but I chalked it up to a daylight savings time issue and didn't bother to investigate. This morning my backup files were stamped as August (which is wrong) of 1992 (which is not only wrong, but really, really wrong). After some investigation it seems that the NetGear time service was messed up. I reset to a different time service, and not only did the 1992 date get corrected by the hour difference was fixed as well.
Hmm, I thought to myself. Was iTunes getting confused because the songs were ripped an hour in the future? I decided to run a few tests. Keeping in mind that since I first encountered this problem, I have never been able to successfully rip and then sync a full disc. Always some seemingly random number of songs would get deleted. After fixing my time server, iTunes worked perfectly.
I have no explanation for this. But I would suggest that if you're storing your iTunes media on a different computer than what you're syncing from, that you carefully check to see that the time settings are the same on both machines. Later on (when I'm bored) I will go back and "break" the time setting on my NetGear storage device once again and test some ripping, just to see if the problem comes back. But for now things seem to be working.
Go figure. Never would have figued this out without the "1992" screw up from NetGear this morning.