Please try AnyDVD 7.3.7.4. Let me know, if it works correctly.
I used version 7.3.7.4. It created an .iso copy of Red 2 of 7,478,208 kb.
I mount the .iso with VirtualCloneDrive 5.4.6.0 and it appears to mount successfully without showing any duplicate titles.
I use HandBrake 9.9.5530 64bit Version. I load VirtualCloneDrive and load the .iso file for Red2. I choose it for my Source and select Title 49 (01:55:43) as the source title.
I indicate for HandBreak to save to a temp folder on one of my internal hard drives. I deselect the Subtitles since I don't want to encode them with the movie files.
When I select Start in HandBreak, it Prepares to Encode for about 1 second, then goes back to green with a Queue Finished message and an output file in my temp output directory for the .m4v that is only 4k large.
Still in in Handbreak, if I change the Source to Title 5 (04:24) and click start, it goes through the encoding process for about 30 seconds and makes an output .m4v file that is 36,513kb large and plays in Windows Media Player if I click on the file, so it appears to have worked.
The problem is with title 49 not being encoded. Something is wrong with it when HandBrake gets it that prevents it from encoding the output file correctly, but other titles on the same disc work seem to work o.k., so I'm wondering if it is a problem with the copy protection on the Red 2 disc for the main movie title 49 that is having a problem when AnyDVD gets it.
Do you want another log file from my 7.3.7.4 version to show what is happening on the AnyDVD HD end when it starts work on it?