Thanks Mediavets, I have tried this and you're right, it's not working, the two images are still different. If templates don't lock the distortion in then what is it they actually do?
They are used to assist the control point detection system.
Normally APP/APG has no 'knowledge' of the relative positions of the images, it just looks for matching points between each and every image.
As I understand it the template provides APP/APG with a 'knowledge' the relative positioning of the images and restricts the detection system to looking for matching points between adjacent images. But it still looks for CPs and applies the optimiser which may relocate images form their template locations.
PTGui's templates work differently I belive and can be used to stitch panos based solely on the positioning data in the template. You need a pano head that is very precise for this to work reliably with different images sets. Most are not sufficiently precise.
Interestingly I've noticed when I stitch the original pics then open and save each pic in photoshop as a jpeg and stitch again, the result is different. Obviously the saving process is affecting some aspect of the picture.
The control point detection system used by APP/APG is very 'sensitive', even small differences in images will result in a different stitch.