Things to check:

1. The depreciation goes to 8829, not directly onto Schedule C.  Is it showing up on Line 42 of Form 8829?
2. Is the Home Office Deduction showing up on Line 30 of Schedule C?
3. Are you accidently using the Simplified Method
4. Check if the Asset Entry Worksheet is assigned to the 8829, and that it is assigned to the proper Schedule C business that you are working on.
5. Is the Home Office deduction being limited by the amount on Line 8 of Form 8829?