Hi,
I am assuming this is an error and not a warning.
Are you using custom attributes in SSPs? What happens when you reboot the ACS (assuming you are using ACS backup in a temporary environment) and try again? Are you able to import the SSP's successfully to ISE?
Will be good to use the latest version of the migration tool. We keep publishing patches with new tool bundle for different ISE versions. So please download the latest if not already.
Migration tool also has logs file in the folder you download and unzip the migration tool bundle. Please take a look at that as well. Also you can open up a TAC case.
Thanks
Krishnan