I had the same issue. Turned out to be permissions. When the file is uploaded by the service account, the service account is set as the owner, and then you can't see the files from the Drive UI. I found the solution online (but can't seem to find it again...)
This is what I did...
It's C#, your question didn't specify. The code you're interested in is the permission stuff after you get the response body after the upload...
FilesResource.InsertMediaUpload request = service.Files.Insert(body, stream, "text/plain");
request.Upload();
//Start here...
Google.Apis.Drive.v2.Data.File file = request.ResponseBody;
Permission newPermission = new Permission();
newPermission.Value = "yourdriveaccount@domain.com";
newPermission.Type = "user";
newPermission.Role = "reader";
service.Permissions.Insert(newPermission, file.Id).Execute();
The file was visible on the Drive UI after this. I tried specifying "owner" for the role, like the api suggests, but I got and error saying that they're working on it. I haven't played around with the other setting yet, (I literary did this last night). Let me know if you have any luck with any other combinations on permissions.
Hope that helps