I thought it might be a bug with the particular scenario (or perhaps map, or even core file) that I was working on.....I'm still messing around with a much larger CM:A project and so far I haven't encountered the same issues in testing.
Not saying I won't have issues as the project progresses, but so far things have been OK.....Haven't touched it in a while, mostly been doing real world stuff, plus a few bits for Heaven & Earth.