There are two versions of Transformers. One has Dolby Digital HD audio for the main track and the newer version uses DTS HD MA audio.
What type of audio do you see as the HD stream?
Does this movie have one big M2TS file as the main movie, or is it split into many different m2ts files? Look in the movie you have decrypted with AnyDVD HD, inside the BDMV-->Streams folder and check this out. If the main movie is split into many different files, you should see nothing that is more than 20gb in size, but many files that are in the 6 to 12gb range. One quick way to find the big M2TS file is to right click inside the Streams folder in a blank area and select Sort by Size.
If there is one big M2TS file for the main movie, you can use tsMuxeRGUI to look at the file and see the audio streams. (I'm trying this path instead of ClownBD). You can download tsMuxeR with this user interface here: http://www.videohelp.com/tools/tsMuxeR
To use tsMuxeR, click on the tsMuxeRGUI executable, which brings up the main window. Click on Add and navigate to the large M2TS file in that Streams folder. Once it is in the program you will see a list of the video, audio and subtitle streams that are available. What I want you to do is remove all the check marks next to the streams except the HD audio and the video. The video should be the very first stream listed.
Now under Output in tsMuxerGUI, I want you to select Demux. Also set a path to a folder on your hard drive where you want to put the demuxed files. Do this by clicking Browse.
I'm including a picture of tsMuxeRGUI in action as illustration only:
Click on Start Demuxing to let tsMuxeR do its job. Once it is finished, you will have a separate file with the audio only and another file with video only. Test the audio in whichever player you like. I normally use VLC media player for this. If you have captured the English audio that you want, we are halfway home. You can then import the two streams back into tsMuxeRGUI and then set it to make a blu ray output.
But all this depends on the movie having one big M2TS file. I'll wait and see if it does. If all this sounds tedious and a bit dumb, it is. This is not a normal process for working with blu ray. But it is one way of making certain that you are getting the correct audio stream.
If you aren't getting the correct stream, you can go through each English language stream shown in tsMuxeRGUI separately, till you find the right one. You can just select each audio stream to demux, you don't have to demux the video again.
None of this gets the movie compressed of course. I'm just trying to get you to the point you can successfully use BD Rebuilder.