Hi Ben
Sorry you’re having issues. I just tried the same thing here, I launched Photoshop via SG Desktop, saved a new file to my desktop as a psb, and then opened the save app via the Shotgun panel.
Then in the save app I selected a task on an asset and saved the file (as a psd). The file saved into the correct location and the name changed accordingly. I didn’t get the Photoshop save as window poping up.
What your saying sounds unintended, but I’m not sure how to replicate it. I was on Mac, so I’ll boot up a VM and try on Windows just incase.
As for manually saving the file in the correct location, that should work, but you have to get exactly the right location and naming so that the file path conforms to the template, otherwise it will discount the file. As a test you could try creating a new file via the Shotgun open app, and then saving it, and see if the path or naming differs?
I’ll let you know once I’ve tested Windows.
Thanks
Phil