Settings seem to be fine.
When stretching idx/sub-subtile Hybrid only takes the idx files and copies it's content and adjusts the time codes, in your case by a factor of 25/23.976=1.0240.., saves a new subtitle file and copies the sub file.
Background info: the idx file contains the location of the subtitles inside the sub file and the time code when to show it, the sub file contains the subtitles.
Looking at the calls, Hybrid uses:
Audio extraction:
"C:\PROGRA~1\Hybrid\64bit\MKVEXT~1.EXE" tracks "D:\Uncompressed Rips\Scrubs\Season 4\Scrubs - S04E02 - My Office.mkv" 1:"D:\Compressed Rips\Temp\iId_1_aid_0_lang_en_12_32_27_6710_01.ac3"
Audio filtering and reencoding:
"C:\PROGRA~1\Hybrid\64bit\ffmpeg.exe" -y -threads 8 -loglevel fatal -i "D:\Compressed Rips\Temp\iId_1_aid_0_lang_en_12_32_27_6710_01.ac3" -ac 2 -ar 48000 -f sox | "C:\PROGRA~1\Hybrid\64bit\sox.exe" --multi-threaded --temp "D:\Compressed Rips\Temp\12_32_27_671002" --buffer 524288 -S -t sox - -b 32 -t sox - speed 0.95904000 | "C:\PROGRA~1\Hybrid\64bit\ffmpeg.exe" -y -threads 8 -f sox -i - -b:a 192k -ac 2 -ar 48000 -channel_layout stereo "D:\Compressed Rips\Temp\iId_1_aid_0_lang_en_12_32_27_6710_02.ac3"
Video decoding and encoding call:
"C:\PROGRA~1\Hybrid\64bit\ffmpeg.exe" -y -loglevel fatal -threads 8 -i "D:\Uncompressed Rips\Scrubs\Season 4\Scrubs - S04E02 - My Office.mkv" -map 0:0 -an -sn -vf zscale=rangein=tv:range=tv -pix_fmt yuv420p -vsync 0 -f rawvideo - | "C:\PROGRA~1\Hybrid\64bit\x264.exe" --crf 20.00 --profile high --level 4.1 --direct auto --sync-lookahead 21 --qcomp 0.5 --no-mbtree --partitions i4x4,p8x8,b8x8 --no-fast-pskip --subme 5 --trellis 0 --weightp 1 --aq-mode 0 --vbv-maxrate 62500 --vbv-bufsize 78125 --sar 16:15 --qpfile "D:\Compressed Rips\Temp\Scrubs - S04E02 - My Office_12_32_27_6710_07.qp" --non-deterministic --range tv --colormatrix bt470bg --demuxer raw --input-res 720x576 --input-csp i420 --input-range tv --input-depth 8 --fps 24000/1001 --output-depth 8 --output "D:\Compressed Rips\Temp\12_32_27_6710_08.264" -
I see that sox uses a factor of 0.95904000 (23.976/25) instead of 1.0240.. (25/23.976) that the subtitle stretching is using. So either one of them seems to be mixed up.
Is it only the subtitles or does the audio also go out-of-synch with the video?
If one of them is correct I can adjust the other to use the same stretch factor.
Cu Selur