I'm getting the same results with PS3Mediaserver 1.10.5, compiled my own ffmpeg on debian 5.0.
Part of the output from ffmpeg -i on a file that shows correctly in the media server:
Stream #0.0(jpn): Video: h264, yuv420p, 1280x720, PAR 1:1 DAR 16:9, 23.98 tbr, 1k tbn, 47.95 tbc
Stream #0.1(jpn): Audio: vorbis, 48000 Hz, stereo, s16
Stream #0.2(eng): Subtitle: 0x0000
And part of the output from a different file that does not show it has a subtitle track:
Stream #0.0(eng): Video: h264, yuv420p, 1280x720, PAR 1:1 DAR 16:9, 23.98 tbr, 1k tbn, 47.95 tbc
Stream #0.1: Audio: vorbis, 48000 Hz, stereo, s16
Stream #0.2: Subtitle: 0x0000
Since it doesn't show it has a subtitle track i can't play it with subtitles, even trough the transcoding folder. However it shows up with undetermined audio track. Before i had this working on a different machine after setting up "und" as audio and subtitle preference/priority. Maybe i'm missing something with the compilation of ffmpeg?
If anyone who reads this has any ideas what to try i'd like to hear it, i've been trying to solve this for a couple days now and its beginning to give me headaches

Maybe i should try it out on Ubuntu again, seemed to work there.
[edit] i've added the debug.log from my machine
[edit2] ffmpeg info:
FFmpeg version SVN-r18855, Copyright (c) 2000-2009 Fabrice Bellard, et al.
configuration: --prefix=/usr/local --enable-gpl --enable-nonfree --enable-shared --enable-postproc --enable-avfilter --enable-avfilter-lavf --enable-pthreads --enable-x11grab --enable-bzlib --enable-libamr-nb --enable-libamr-wb --enable-libdc1394 --enable-libfaac --enable-libfaad --enable-libfaadbin --enable-libgsm --enable-libmp3lame --enable-libnut --enable-libschroedinger --enable-libtheora --enable-libvorbis --enable-libx264 --enable-libxvid --enable-zlib
libavutil 50. 3. 0 / 50. 3. 0
libavcodec 52.29. 0 / 52.29. 0
libavformat 52.32. 0 / 52.32. 0
libavdevice 52. 2. 0 / 52. 2. 0
libavfilter 0. 5. 0 / 0. 5. 0
libswscale 0. 7. 1 / 0. 7. 1
libpostproc 51. 2. 0 / 51. 2. 0
built on May 16 2009 16:58:51, gcc: 4.3.2
[edit3]
ok, i've just tried it out on ubuntu 9.04 and there ffmpeg shows me the same thing for the files, but now ps3mediaserver sees an undetermined subtitle on the faulty file, seems ffmpeg is not at fault here.