After some searching of the Scooter Software forums, I found this post: http://www.scootersoftware.com/vbulletin/showthread.php?t=10928&highlight=align which essentially tells me that alignment doesn't work for non-text files.

I found two workarounds. One was to save my Excel files as text and then compare them. The second, after reading the forum answer several times, was to change the field used as a key field. That was easier, and in my case, made the alignment no longer an issue.

I found this post Align with option not available unless using text based files in the Scooter Software forums. It essentially tells me that alignment doesn't work for non-text files.

I found two workarounds:

1. Save my Excel files as text and then compare them.
2. Change the field used as a key field.

The second workaround was easier, and in my case, made the alignment no longer an issue.