I'm currently working with some shapefiles for Mars data and have reprojected a geology shapefile to a THEMIS layer. The Projected Coordinate Systems are the same, however, the extents are not. It seems that after projecting the shapefile, the extent changes and centers the shapefile to the THEMIS layer. So I end up with a tiny shapefile about 1 pixel in size in the centre of my rasters.
Did you use the Project tool or ArcMap (and then export the data using the data frame's coordinate system)? Or did you use the data's property page from ArcCatalog or the Define Projection Tool? If the latter, that updates the metadata only and doesn't permanently change the data's coordinate system.