It sounds to me like the projects with the alignment problems are non square pixel projects. If that's the case you are facing the problems that cropped up with Adobe change the NTSC D1 par from the old .9 to the new .91. This shift would be minor. However, if your D1 or DV sized projects are actually widescreen then the shift would be more pronounced.
The other thing that could be happening is that AE could be mis-interpreting square pixel comps (Illustrator is always square pixels) as non-square. This would also throw off the horizontal positioning.
This is why I always work in square pixel comps, even when I'm working with non square footage.
If you can't figure it out post a link to a file and I'll take a look at it for you.
Hi Rick. That was one of the first things we looked for. It isn't that unfortunately as everything is in square pixels. None of the ojects are at all distorted or proportionally changed as well...all of the bits look exactly as they should, they are just in the wrong place. Thanks for the idea though
Are you able to open a project in both versions and confirm that the layer positions and anchor points are unchanged numerically? If the numbers are identical, it's almost certainly some kind of interpretation issue.
Hi Andrew. It would seem, that when comparing the two, it is a potential Illustrator issue...or the way Illustrator files are being brought in. The positions are exactly right for all layers, however any layers that are Illustrator assets have anchor points in the wrong place horizontally. I figure it is something to do with the way After Effects CS6 is dealing with our old Illustrator 3 and 4 assets, which is quite painful. Hopefully there is some workflow to convert that won't be too crazy for us to fix them...it is a bit annoying that it is two Adobe file formats talking to each other in a completely different way from the way they used too.
Thanks for the idea...I think we know the problem now, if not the solution
At least After Effects snaps the anchor points with the command key now.