Have noticed that at present (version 2286) MeGUI can't handle intact trueHD audio tracks.
Here's a method I use to do so - hope it helps:Re-Authoring Blu-Ray Main Movies With Intact TrueHD Audio Sound Tracks
Instead of only extracting the lossy TrueHD core (640 Kbps AC3 audio), or converting the TrueHD track to FLAC or DTS (requires payware for DTS, FLAC has device compatibility issues), the method below preserves the original lossless Blu-Ray TrueHD audio track.
1. Decrypt with DVDFab Passkey.
2. Load MeGUI.
a. Go to Tools\HD Streams Extractor.
b. Extract all required streams from the main movie playlist (*.mpls) file.
3. Load mkvmerge GUI.
a. Add .264 video stream, all required audio streams including the .thd (trueHD audio) track extracted in step 2b.
i. Use multiAVCHD to create chapters and subtitles; it’s easier than mkvmerge (see step 5).
b. Mux mkv file.
4. Load Clown_BD v0.79.
a. Add mkv file created in step 3b.
b. Choose M2TS container format option.
c. Clown_BD demuxes mkv streams, then remuxes to M2TS container with TrueHD audio.
5. Load multiAVCHD v4.1 build 771.
a. Add M2TS file created in step 4.
b. Click on “Subtitles & Audio” tab.
i. Uncheck the 2 TrueHD audio conversion checkboxes. Don’t want it converted!
ii. Click title to open extended properties.
iii. Load external subtitles extracted in step 2b.
iv. Browse for chapter file extracted in step 2b.; load chapters.
c. Go to Menu tab
i. Reset Headline text to authored Movie title.
ii. Check create chapter menu pages for one title.
1. For many title compilations, better to uncheck this.
d. Click START button on main menu page.
i. Choose “Blu-ray Disc” option.
e. Let compilation finish (takes 10-20 minutes on a decent quad core).
6. Rename AVCHD folder created by multiAVCHD compilation to Blu-Ray title name.
7. Load blank blu-ray disk.
8. Load ImgBurn.
a. From “Ez-Mode Picker”, choose “Write files/folders to disc”.
b. Choose top level blu-ray folder renamed in step 6.
c. Click “Build” button.
9. When burn finishes, you’re done!