Most likely the backup was via Desktop Manager and that does not back up apps or themes unless you use the "transfer device wizard." It backs up data and settings.
Or if you used something like bbsak to back up the apps (cod files).
The other possibility is that if you did a OS upgrade, sometimes a backup of apps might occur but I'm not sure where to find them. You could search your computer for *.cod files and see what turns up.
