Berry120 did you get toolnix from bunkus.org? Just wanting to make sure I got the right one from the right source.
Yup, that's the one.
FWIW, I don't tend to use this to mux subtitles into mkv's directly, I tend to use handbrake to re-encode into h264, and put the srt file in as part of that process. But I have used mkvtoolnix for this in the past, and extensively for other tasks (such as extracting the sub files from the raw DVD rip to then OCR into srt format) and I haven't had a problem with it.