Thanks. I have tried the repair as well. Still no love… I have found a work around now. Export compressor as standard 90min DVD file, m2v and ac3 files, then import into MPEG streamclip and Mux the files. you have to name both files exactly the same name (except the extension) and keep in same folder, then drag into MPEG Streamclip the .m2v file and export to mpeg with mp2 audio. You cannot put the bit rate above 9000 but it is good enough for this one. I think the issue is somewhere in the Muxing stage of the compressor process.
What a pain, but it will work for this job. I will do a fresh install soon!
Thanks for the help