Currently our Drupal 5 to Drupal 6 upgrade path does not work for FileField. It does not enable any of the previously used FileFields and their "status" is left at 0 in the database, effectively making all FileFields disappear.
Generally speaking this is usually fixed with a call like this:
We also need to use the "safe" version of content_fields() during the upgrade, since content_fields() won't list any fields that are disabled. Instead we should use content_types_install(). This patch corrects these problems and restores the upgrade path from Drupal 5 as far as I've tested.