When using %script% as a command line of an execute command and inserting a script that is bigger than 64KB on the Script tab of the Execute Command task, the script will be truncated to 64KB of data after saving the task.
The Visual Basic control used for this field has a 64 KB restriction. VB truncates the contents of this field to 64 KB without any warning. This is by design.
For scripts larger than 64 KB load them in the Database as a custom resource and on the command line specify the script to run from the custom resources location.