if you still don't see the notes box window - make sure the little music icon in the clip section is highlighted to show it.
otherwise.. not sure.
hmmm I think that was already selected but I changed something earlier on and it hasnt changed back yet. So I shall see what it will do tomorrow once I work on it again.
Thanks for the help as of now
If you click on the midi clip that's giving you the issue, and make sure you have the midi view selected at the bottom (not the one that shows your plug-in/effects, but the one that let's you input midi information) you will see some boxes in the very bottom left of your screen. By default it should have a box titled clip and a box titled notes (If notes isn't showing, look at the bottom of your clip box and you will see three circles, one with an "L', one with a musical note, and one with an "E" Click on the one with the musical note so it turns yellow and you will then see you Notes box. At the bottom left of the notes box you will see a header that says "Pgm Change", and at the very bottom of that there is a tab for "Pgm ---". My issue was that it has a number at the side of it which corresponded to a certain preset in my synth, so whenever i stopped playing, it reverted to that particular preset. To solve the issue i just right clicked and reset the value to blank.
Hope that helps mate