If the software used to work fine before, it should work the same now since it works ok for documents and prints. It sounds like you just need to relearn how to use it and deal with any quirks like you are experiencing now. If you don't want to invest the time in that software, you could always switch over to Vuescan, learn that and then know you will most likely be able to use Vuescan on any scanner you use in the future since Vuescan works on most scanners.
Doug