OK. I've found out what was causing this. If MB has a small window size when restored down is implemented, it will resize the left and right panels (or the centre, main panel) and when maximised it will display the behaviour in my post above. I have increased the restored down window size to almost full screen, and when I do this, it resolves the problem. Basically, as soon as you drag the maximised window, it shrinks to whatever restored down size it has in memory then, when maximised, it retains the restored down size for it's panels.
I'm pretty sure this is a bug, or at least an undesired effect. Hopefully Steven will get to see this post and tell me what's happening and whether it could be fixed/changed.