Good point Peter - had not considered that.
I use APT to focus (and capture control) with the Canon 5D MkII (yeah, I'll go CCD one day!), and use the crosshair overlay as my alignment centre (just like a crosshair reticle) AND my focus tool (I find it MORE accurate than any Bahtinov). I think perhaps the star had drifted slightly that I was using to focus, and would no longer be centred in the field or on the chip, so would illuminate and shadow the secondary to one side.
Thanks for that - might have talked my way through it