It appears that IconPackager is failing to load the path to some of these icons, from within the program.
For instance, I have a custom icon for VBS scripts, which I simply cannot assign from within IP, but I can assign it by using the property page and changing the icon there!
IconPackager is failing to correctly assign paths for at least some of these icons that it's failing to change. If I look at the "File Name" (sic) line above the icons and cursors window in IP for these unassigned icons, instead of getting a path there's an entry like ",0" rather than "*path and filename*,5".
[edit]
On reopening IP and looking at the missing icons, the filename is listed as being "C:\Windows\System32\,0".
Do those of you with the same problem see the same, or similar, error in filename?