Geoprocessing task not using provided file paths

[DevonCanady]

I have a geoprocessing task on ArcGIS Server 10.1 that uses arcpy's Select By Location on a number of layers and writes a SQL file based on the results. For each iteration of the selection I'm passing a path to where the layer is located yet I'm getting this error:

ERROR 000732: Input Features: Dataset C:\arcgisserver\directories\arcgissystem\arcgisinput\RegQueryBuilder2\RegQueryBuilder.GPServer\extracted\v101\tigerdata\Zips\esriZipsLayer_NAD83.shp does not exist or is not supported

I'm wondering why the task is looking in this folder when I have hardcoded file paths (not env.workspace) in the script. I tried setting the workspace and scratch workspace environments in the initial execution of the script tool which was used for creating the geoprocessing package but I got the same error.

PS: I had worked around this error by copying the layers to that folder location but since the layers are very large it won't work for production.

[JoshuaBixby · Accepted solution]

Regarding the hard coded paths you originally tried, were those paths accessible by ArcGIS Server:  About registering your data with the server - ArcGIS Help 10.1 

[DevonCanady]

Joshua Bixby‌, in regards to this thread I gave rw permissions to the ArcGIS Server account on the machine hosting the files the script is accessing. After doing so I was able to register the input/output folders in Server Manager, however I'm still getting the same error as before. While I'm sure I did need to do these steps, I'm still not sure why it is looking in that folder for the data when I have provided a completely different path.