I am running ArcGIS 10.2 Desktop
Several different models I have built and tested successfully previously are demonstrating the same problem. They appear to execute slightly to the South of the indented location.
All the tools work by taking several shapefiles, converting them to rasters as defined by an extent raster, and then doing some "stuff" to the rasters before outputting a single results raster.
The image shows one of the examples the red polyline file and the green polygon file should be processed within the boundaries of the blue raster. The actual result in black is slightly below.
I have checked the spatial reference of all the inputs and the data frame and they are all the same. So I am perplexed as to why this is happening.
As I said all the models work on other datasets that I have used. I have gone back and done some test runs and the models are fine. I suspect it is something to do with the input data but I don't know what to check for. I get no warning or error messages when running the models.