What options did you use when saving the TIFF file? I would have expected that if you have compression set to None, it would save an identical version.
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If you use auto-align a lot, you will soon discover that the result is frequently offset by 4 or 5 pixels. Once nudged into position, the match is usually perfect - so it's not that the algorithm itself doesn't work. I'm willing to bet that's what happened here.
The offset appears random and can go either way, often diagonally, such as two pixels right and four up.
I've no idea why this happens, but I always factor that in. Once completed, I go to 100% and nudge into place. Only then do I run auto-blend if that's the next step.
This is also one reason I never use Photomerge.
it would save an identical version.
The TIFF is identical as you can see from the second auto-align because the Difference blend is BLACK. The problem is Auto-Align didn't work correctly the first time.
I could understand if you were auto-alining two DIFFERENT tripod shots for instance but this is a RESAVE of the SAME photo and I expected it to be dead-on the first time. I guess I will just have to do the Auto-Align twice from now on as that seems to work, at least in this occasion. You would think an operation that is used a lot like ALIGNING would work better.
Yeah, but there's no guarantee it won't be offset the second time as well. It's totally random. Much better IMO to just check at 100% right away and be done with it.
I should stress again that the algorithm works. The match is perfect aside from the offset, so there's really no reason to run it twice.
I wouldn't say the algorithm works if it is OFFSET, especially in the scenario of an identical photo. In my example above it should be considered a bug. Why did it work the second time? The algorithm should be working the same.
As I said, the offset is random. Happens this time, not the next.
Yes, I agree it's a bug. I just hasn't bothered me all that much, because I like to double check alignment in any case. There are many scenarios where you would want to nudge a pixel or two even if it did work as expected - for instance to compensate for parallax errors.
Now that I am aware of this problem and have been checking more it seems like it is BADLY unaligned MOST of the time on the first try but works well on the second try of auto-align. My example in the original post is essentially the same photo and it can't even do that well. Adobe needs to work on this.