I don't want to wade into the swamp of limits on charitable contributions based on AGI, especially when there are carryovers, but this is from Pub 526:

Noncash contributions to 50% limit organizations. 

If you make noncash contributions to organizations described earlier under First category of qualified organizations (50% limit organizations), your deduction for the noncash contributions is limited to 50% of your AGI minus your cash contributions subject to the 60% limit.

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Without some real numbers to work with, I'm not sure how this applies to your situation.  It could be that the software is trying to save your bacon, while you are trying to fry the software.