Well, I'm actually not sure what "stock" means in this context. Or root for that matter.
After this is resolved, I'm pretty sure I'm only going to perform OTA updates.
A stock phone would be a phone that came from the store and was unaltered by you. It sounds like this is what you have.
A rooted phone is one that had had its operating system replaced so that you have administrator access to all the files, meaning you can replace or edit any of them. A stock phone has this locked down. Sort of like at some workplaces you can't install whatever you want on a computer the Droid phone comes default, or stock, with a regular user account and not one with admin, or root, access.
A rooted phone lets you theme the phone more, lets you overclock the CPU, use wifi-tethering where your laptop can connect to the internet through your phone's cell-tower connection, and lets you do some other things too. Rooting your phone also voids your phone's warranty.
There have been cases where something is wrong with the phone. I bought my phone in November and had to return it in January because it wasn't functioning correctly. It sounds like this may be the case with yours, which is why I suggested stopping by a Verizon store if what is occurring is easily reproducible.
Disappearing icons:
There are a couple of threads here where folks have had the same problem with the background showing up but no icons. I replaced my icons when it first happened and then a day later I had them doubled up. I'd delete an icon and another one was underneath. Not always the exact same ones as I didn't replace the missing ones in the exact same place. It probably happened to me 3-4 times in less than a month. A Verizon rep told me they thought it was due to the background showing up on top of the icons instead of the reverse and it being due to the "wrong" type of wallpaper. A reboot always fixed it for me. I do not know what fixed it for good for me but I haven't had the issue for a few months now. I have rooted my phone so all my previous settings have been wiped and replaced.
So here are my suggestions...put off rooting for now:
1) replace your wallpaper with one of the default ones and see if the problem goes away. This would be the easiest less intrusive option.
2) Use ASTRO to back up your installed apps to your sdcard. And then reset your phone. Settings - Privacy Settings - Factory Data Reset.
Option 2 means when you power on your phone again you will have to enter your gmail userid and password. This will resync your phone. You then can download Astro from the market again and use it to reinstall your apps from your sdcard. Some of the data in your apps may need to be re-entered. Txt messages probably will be gone. Verizon can do this reset for you in one of their stores, over the phone, or you can do it yourself.
The icons not displaying on the desktop issue won't be a hardware one, so Verizon probably won't swap the phone out for a new one, and if they did your settings would be gone anyways.
As for the update it probably got downloaded to your phone and installed without you knowing it, although I'm curious what happened in January to make you think you got an update then.
Let us know how you make out.
