1. Re-rerun the compare with more 'Ignore' options
2. Make sure the Properties panel is visible and the 'Track focused object from panel 'Properties' ' is toggled on
Please see attached document for more detailed instructions along with screenshots.
If, after trying the above steps, Toad is still showing differences that are not clear to you, please create a service request and Quest Support will assist to troubleshoot this further. In order to do this, they will require the schema compare snapshot files for both schema. Run the ‘Schema Snapshot Wizard’ (see document for instructions) to produce these files, and attach these files to the generated service request.