Using civiCRM 1.7.9682 and Drupal 5.1
Steps to recreate:
1) Go to Advanced Search.
2) Choose your Search View, Contact Type, Group.
3) Also choose a Custom Field to search for.
4) Click Search, and on the Search Results page, create a Smart Group based on the search results.
5) Go to Manage Groups, find the Smart Group you've just created, and view members.
6) You should see that everything in the Advanced Search was saved as a criteria for the Smart Group EXCEPT the Custom Data.
Essentially, the Smart Group criteria won't save the Custom Data operator. This wasn't a problem in previous civiCRM versions.
Any help is appreciated.