Hi Katy,
If you're using 10.1, we check the data extents against the transformation and GCS (source/target) extents. Maybe you're hitting that. Try projecting the data in ArcMap instead by including some layers that worked fine. Once the data's added, the data frame is set to the target coordinate system, and the transformation is set, right-click the layer and select data, export data. In the new dialog, toggle it to use the data frame's coordinate system.
If it does look like you're hitting an area of use issue with the transformation, would you mind sending me the extents of the layers you're having problems with? I can double-check what we're doing, and possibly ask that the area of use for the transformation or the GCS be revised so this data would work correctly. mkennedy at esri dot com
Melita