The only thing I have done to my computer today is change some sharing settings so I can access files from my ipad could that be it? Because now the sequencer that was working perfectly wont work either?
If you look in the directory where the msq file sites (normally under Documents\My Lightshow Sequences), do you have any .bak files there? Hopefully upon every save, it's been creating a backup file. If this is there, grab the latest one and rename it to .msq and see if you can at least get everything back from the last save.
Al least that's a starting point. I spent this week remaking an existing sequence from scratch after the sequencer and the scheduler decided that the sequence was 1:53 long, where it was really 2:35. It would speed up my sequence to fit the 1:53 timeframe, and then there would be 40 seconds of no lights while the music finished. No matter what I did, it wouldn't fix itself. In the end it was quicker to remake it.