I'm having a similar issue so I figured I'd come with some examples.
Here is an example of very good alignment. This is two stacked images showing the difference between them in photoshop. These images were taken very close together, but I did have to do some manual adjustment in photoshop to get them to line up properly. Once aligned, you don't see any corona lines, only outlines of prominences/etc, and only a faint and broken ring of white, all indications that they're lining up well.

Here is the same thing, but from much later in the sequence. Again, I manually lined up the images so the circles overlapped as much as possible, but now you can see things like the promineces don't line up perfectly and you can a lot of corona lines as well. I'm not really concerned with promineinces, especially when building a corona shot since they'll be blown out anyways, but I think they're evidence that the alignment isn't perfect. I tried doing some manual rotation on the layers, but it didn't really help. Better aligning one part of image seemed to thrown off another. For example, you can see that the base of the flare (?) at about 2 o'clock is all black in this image, so that point is very well aligned. Meanwhile, the small prominence at the top and the large one around 4 are both slightly off. If I rotate the layer a bit to line one of them up, another feature will be misaligned.

I have to imagine that if there is a good way to line these images up, it would require some kind of manipulation beyond just moving and rotating layers, but I don't really know where to begin. It could be that there really isn't much hope for aligning images from minutes apart on a static tripod.
Any thoughts?