First a bit of background for those who may not know what NEO-FFI is...
NEO Five-Factor Inventory (NEO-FFI) is a shortened version of the NEO Personality Inventory (NEO-PI) now in its 3rd edition (NEO-PI-3). Both inventories were first published in 1985 and now the NEO-FFI is also in its 3rd edition as of 2005 (NEO-FFI-3).
NEO-FFI-3 measures the "Big 5" personality traits (Neuroticism, Extraversion, Openness, Agreeableness, and Conscientiousness), comprises 60 items and is designed to take 10 to 15 minutes to complete; by contrast, the NEO-PI-3 takes 45 to 60 minutes to complete.
Both NEO-PI and NEO-FFI were originally developed for use with adult men and women without overt psychopathy.
Now onto the question of difference between the 2nd and 3rd editions
The latest revision of the NEO-FFI involved the replacement of 15 of the 60 items to improve readability and psychometric properties. The revised edition is now thought to be more suitable for younger individuals and is also thought to have a stronger factor structure and increased reliability (McCrae & Costa, 2010).
For further reading, see the NEO research bibliography
McCrae, R. R., & Costa, P. T., Jr., (2010). NEO Inventories: Professional manual. Lutz, FL: Psychological Assessment Resources, Inc.