Since it is seeing commercial disks and some homemade dvds then it has to do with being compatible only with some brands of disks. Usually you can get a firmware upgrade for a burner that incorporates new compatibility with current disks, but not with Apple (sigh.)
Try TDK DVD-r, they're generally more compatible. DVD+R probably won't work at all. Some thing applies to CD-R, some brands will work, others won't. Imation may work.
In general, if you're going to be burning a whole bunch of DVD-R, you're better off putting together an external firewire burner (not USB, since the iBook will be USB 1.0 only). All Superdrives are slower than external burners. Makes a huge difference when you have an external 16X burner connected via firewire.