That is because you should have been depreciating those improvements even though the house was fully depreciated.
It is too late now to correct this in a simple way. You will need to file Form 3115. Also, you may have assigned the house a salvage value.
Straight Line Method
Before 1981, you could use any reasonable method for every kind of depreciable property. One of these methods was the straight line method. This method was also used for intangible property. It lets you deduct the same amount of depreciation each year.
To figure your deduction, determine the adjusted basis of your property, its salvage value, and its estimated useful life. Subtract the salvage value, if any, from the adjusted basis. The balance is the total amount of depreciation you can take over the useful life of the property.
Form 3115
Unfortunately the depreciation recapture is "allowed or allowable" meaning even if you never depreciated it, you would still have to recapture the depreciation. Depreciation taken would be on line 18 of Schedule E.
One solution is to elect an accounting method change and file a Form 3115 in the current year and take the prior depreciation as a section 481(a) adjustment. [land value is separated, land is not depreciated]
Below are the IRS links related to the change in accounting method. TurboTax does not have that form.
May be these will help
Form 3115, Application for Change in Accounting Method
http://www.irs.gov/uac/Form-3115,-Application-for-Change-in-Accounting-Method
Instructions for Form 3115 (03/2012)
http://www.irs.gov/instructions/i3115/index.html
Form 3115,
http://www.irs.gov/file_source/pub/irs-pdf/f3115.pdf
