Well, I don't know if this is a GingerBread specific issue or not, but I started to notice it in the first leak of Gingerbread I installed, (.573) and it seems to carry on to .596.
It took me a little while to figure out what was really happening, since I do not shut down or reboot my phone too often, (unless I'm installing ROMs or something. ) But I started to notice I would occasionally be missing an app shortcut or two on my home screen. It would always be the same app, and I could add it back without problems, but it would be gone again semi-randomly after a couple of reboots.
I eventually figured out that those apps were installed on my SD card, and that they were not being placed back whenever I mounted or unmounted my card as a portable drive, and then rebooted the phone for some reason.
I moved them back to the phone memory, and that solved my issues.
So now I'm posting this here, in case it can either give a good chuckle to our more experienced members or help some other newbie like me with the same issue.