I use this constantly and I thought that the latest version will fix some of the issues here but that was not the case.
This is what I experience.
Schemas: SC_A & SC_B (Target).
Click on Database, Compare, Schemas.
The only options that I remove are comments (on tables, column, views, etc) and Compare Storage Clauses.
Run the comparison.
It says Objects only in SC_B…and it lists a bunch of tables.
Get the script to drop the tables on on SC_B, run it, all is fine and dandy.
Run the comparison a second time.
Get no objects in SC_B.
Open another TOAD session on SC_B.
And run a compare against SC_A.
First thing I get is: Objects only in SC_B…and it lists a bunch of tables.