To reproduce this bug:

1. Open the attached project
2. Open 'Demo.Unity'
3 It has:
-Empty gameobject with negative x scale (-1)
-Another empty gameobject as its child
4. Select child gameobject ( 'BrokenXTranslateHandle' )
5. Try to change its transform x using handles
6. Notice it increments by integer values (-1, 0, 1, 2, etc...)
7. Same happens when having y,z scales negative
8. Change parent's scale to positive
9. Now child translates as expected using handles

Captured repro: http://screencast.com/t/oowoaEmm