I have a GpService that uses layers in memory and in Scratch Folder and Scratch GDB.
Most of the time the data is written into arcgisserver\directories\arcgisjobs into the gp service directory
Some time the data (or some of the data) is written into C:\Users\mody\AppData\Local\Temp instead.
Some time I see a directory created there and deleted a few seconds after the service finished and sometime it just stay there.
The arcgisserver directory is on a network drive.
Anybody see this problem?
I also see a good number of files in the Temp directory on my GP server (as well as Hosting, but not sure if that helps). I have seen this app data location used for staging by some of the System and Utilities services like offline packaging. Not sure what your GpService is doing, but if you are taking advantage of any other services during the execution of your service those might be writing there.