The association of stationery with sections in ON2003 will be lost after the
upgrade, you'll need to reset this on per-section basis (unfortunately
).
The stationery pages themselves should have been saved into
%appdata%\Microsoft\Templates folder in "My Stationery.one" file. This file
will be upgraded when you access custom stationery form OneNote 2007 for the
first time (e.g. bring up the Stationery pane).
Is that file missing on the machine? Did you happen to upgrade from XP to
Vista (you might need to check the old XP folder then and move the file into
new Vista location, it should have happened automatically, though)? Another
possible problem could be if "My Stationery.one" was corrupt in a subtle
manner, so ON2003 was still limping along but ON2007 fails to upgrade it. In
this case you'd need to open the file with ON2003 and fix it (if you log a
bug to Connect site, you can attach the file to it and we'll take a look too).
-Irina