OK, well i've been doing a bit of searching to try and find out why most people aren't having any problems with adding the new audio but others are. Well it looks like the problem is down to muxman. Some programs installed on pc's seem to have an undesirable effect on this program. It doesn't really like any other operating system than windows xp and can do a few strange things to the output.

I've tried several times to recreate the problem on my pc but everytime it works fine. I had the chance to try it on someone with windows 7 and i have found a solution.

when importing the subtitle files into muxman import all 4 in numerical order, but only if you are having the problems as files 21 & 23 aren't really needed. But doing this won't add any extra subtitle tracks but will enable muxman to behave on problem systems and you will have the correct subtitle tracks displayed on the reauthored file