Chris, thank you so much for your help.  I've been working with the people at the scan center and have realized what the issue is.  For some reason, some of the collected images were lost during the transferring process so that when the final T1 image is being reconstructed, there are missing slices.  This is showing up as varying slice thickness (e.g. 2mm intervals instead of 1mm when there's a missing image).  All the images were collected though, so the solution should be as simple as re-transferring the data.  Thank you again.