There is no significance
Asuna Vesperina Theotanasia Entheofushia, a.ka. Asuna Kagurazaka, has one green eye, and one blue eye, as depicted in every canon appearance except in Negima!? There is no real known significance as to why she has heterochromia, though it may have something to do with the fact she is of royal descent. She is seen as having heterochromia before she looses her memory, so that isn't the cause.
As far as why Negima!? is different, it is because it is a different studio who worked on this project, and they did redesigns for many of the characters. Negima!? actually has a number of differences from the original manga.
That we know of...
Mahou Sensei Negima (the manga) was canceled, so there were many stories that went unexplored. There is a possibility that this is something that the author was unable to reveal because it involved bigger plans around Asuna. Sadly, without speaking with the author himself, there isn't any way to know.