In Leopard and earlier, text in PDFs which used a custom font encoding wouldn’t be interpreted correctly. If you tried to copy and paste it, you would get gibberish. The same problem affected Find, and seemed to addect DEVONthink’s index. Acrobat had no problems with find or copy/paste. This was a big problem for me since I had a large number of old PDFs that I could not find things in.
Snow Leopard has fixed this! I rebuilt my database and now search is working great. Just an FYI for folks who may have had problems finding things.