Can I get JUST the alien subtitles in Star Wars?

Well, if it's true that the stream is labeled properly and you can address with your own build, then I can't imagine why this would be ignored. Question about your build - what is it based off of? The latest Eden beta?

And have you used Pavtube's app at all? It looks like it can separate out the forced sub so this is avoidable

I'm not quite sure exactly why it hasn't been addressed yet. It is in the roadmap under Future/Pending (see http://trac.xbmc.org/roadmap). My guess is that it has to do with the fact that the subtitle decoder is part of the ffmpeg project, and the XBMC developers would prefer that ffmpeg complete their side of the implementation first so that we don't need to use patched ffmpeg sources. Or, perhaps it's because there are just bigger fish to fry. I don't know exactly.

My build is based off the source of the Eden release. It also includes a patch submitted by another user to add bitstreaming of DTS Master Audio and Dolby TrueHD over HDMI, but other than that I'm trying to minimize the changes to keep it as stable as possible.

I haven't used Pavtube's app at all. I prefer to keep my collection in the original format as much as possible. I don't believe I should have to deal with remuxing or performing alterations to the data in any way just to deal with limitations of the player.

Ok I'll give your build a try, then!

Should I uninstall my current install or can I install over it?

I haven't built the installer, so included in the zip file is just the folder structure of what would be installed to "Program Files" (or wherever you install XBMC). As long as you have Eden release installed, you shouldn't have to uninstall. All you need to do is to extract the zip and replace the original exe and dlls, etc. Though, as long as all your plugins, skins, and settings, etc. are in your users directory (C:\Users\[username]\AppData\Roaming\XBMC) and not in the program files directory, you can also just extract this to a different folder and run it from there as well.

This seems to be working well for me!

I also realized that I didn't add subtitles to a lot of my bluray rips. Not looking forward to going through my blurays to get the subtitles.

This actually didn't work for me. I realize now that my Lord of the Rings rips already had the subtitles hardcoded.

I have tried so many differenct configs for Phantom Menace to get this working but in no case can I get the forced subtitles to appear. I removed all subtitles except for the forced and used mkvmerge to set stream as forced "yes". It still won't show.

From what I understand, there are few players that can handle forced subs and it sounds like XBMC is one of them. I assume it supports it when I use your patched version of XBMC.

Is there anything I need to set beyond overwriting the XBMC install with your files?

Also curious - will this only work with a video that is in the movie library? I'm still trying to figure this out and wondering if the reason why XBMC is not playing back the movie with the forced subs is because I'm playing it from a folder that isn't set to movies

It should work with movies in any location. All you need to do is, in the audio dialog, set the subtitle to the stream which has the forced subtitles, and uncheck "Enable Subtitles". The forced setting in MKVMerge should not make a difference. I don't personally have the star wars Blu-rays to test, but I've uploaded a short clip from Avatar which should work. With "Enable Subtitles" checked, you should see the closed captions and the Na'vi translations, unchecked you should see only Na'vi translations. Standard XBMC will display nothing with "Enable Subtitles" unchecked.

http://dl.dropbox.com/u/41591327/forced.mkv

Yeah it does work. How is that you ripped Avatar then? The forced sub you didn't add yourself and tagged it as such? I would have expected to see the subs in mediainfo but it's like they don't exist

I ripped the Blu-ray disc using AnyDVD HD, which provided me the full unmodified m2ts files. Then I used TSMuxer to demux the m2ts files and used MKVToolnix to mux the MKV. For the sample I provided, I also then used ffmpeg to re-encode the video at a lower bitrate so that the file wasn't enormous.