Schema Compare max out at 500 differences regardless of setting, when run by command line or as a scheduled action.
I run schema compare and there are no problems with maxing out of differences.
I create it as an action and I manually run it with the green arrow button, and there are no problems.
But when I schedule the action or run it as command line, I get a message in the log that it has reached a maximum of 500 and not all differences are listed. I did not set the "Stop when # of differences reaches:" setting (under compare's Options | Misc. Options). I specifically increase the setting to 9999 and it still notes as max out at 500.
This is only a problem when running as a scheduled action or by command line.
Issue introduced when the schema compare became an action, starting from version 9.7.0.
Do not schedule compares or run with command line.
Install Toad 9.6.1 and set up the schema compare control file. Then schedule that to run and run by command line based off of that. Please refer to Toad 9.6.1's Help | Content | "Run Compare Schemas from a Command Prompt" for steps on how to create schema compare control files for you to run as a batch/command line.
Waiting for fix in a future version of Toad for Oracle.