I plugged in my D3 for the first time this evening via USB to transfer the pictures off my phone onto my computer. I noticed that several of the icons on my Home screen disappeared, all of which appear to be items I installed in the "Media Area" (whatever that is) section. When I ejected and unplugged my phone, they did not return. What gives?

Because your sd card is being mounted to the pc therefore your phone cannot access the image files

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Speculating of course

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I understand that, but even after proper ejection and disconnection, the icons do not return after the phone remounts the SD card.

They won't unless you can force close your home screen launcher so that it rescans for the apps. A reboot would bring them back. I use Launcherpro, for things like that it has an option to "Restart LauncherPro" which will bring back the apps. Either change the USB connection to Charge Only or just be prepared to reboot after each connection (or move everything back from "Media" to "Phone" for apps.)

Ive had more severe issues where my apps dont restore even after a reboot. My only solution is to uninstall them & reinstall them. It's a pain, and apparently 1.5 GBs is NOT enough for all the apps i want to play with, so I have to push apps to "SD".. or now known as the media storage, which is the other 11.5GBs of partitioned internal storage.