Actually, I've noticed a few things like this of late. Seems like it started after the most recent security update.
1. Files that do not show up on the desktop, or indeed within a finder window, but other applications, such as the ls command in terminal can see them.
2. CDs/DVDs that appear to mount, but do not show up on the desktop or in the finder's left pane. In some cases, other applications, such as DVD player, etc do not notice the CD/DVD was inserted, but again, using commands in terminal (df in this case) shows that the media was in fact mounted, and you can use "cd" and "ls" to see the stuff on the media.
3. After inserting and using a CD or DVD, selecting the corresponding icon from the desktop and hitting cmd-e (to eject) causes the CD/DVD to disappear from the desktop, but the disk doesn't actually eject. You have to go into disk utility, select the optical device entry in the left pane and hit the eject button before the disk will be ejected.
All of this on a g4 powerbook and an intel core duo mac mini
So far, a reboot has always fixed each of these problems, but they happen again over time, even with previously working CDs/DVDs.