Are certain fonts available on the iPod and others not?
Yes. The font selection shown in IB includes all of the fonts installed on the Mac host. Only a subset of these is available on the iPhone. When you select an unavailable font for an iPhone project, IB will just give you the default or the available font that was last selected.
Btw, there are at least two free iPhone apps that will display the available fonts. I have FontViewer.
Font selection in IB can be a little tricky. For example, you might select a UILabel instance, then select a different size or style in the Font window and find the selection doesn't affect the label. You need to "sync" the editor window with the Font window. I've found the best way is to tab through the controls while the Font window is open. At some point you'll see it "catch" and the selections in the window will start to track the selected controls. When that happens, you should be able to tab to the label and make the change you want.