Jenkins auto generates wrong config for composer

Check the diff of config.json between

• your good version after manual fix
• the wrong version as regenerated by Jenkins

That will tell you exactly what is changing (for example, it could regenerate OAuth credentials)

Then check which php-related plugins you have installed (as described in "PHP Continuous Integration Template using Composer and JenkinsCI"), like phing, Ruby, RVM, PHP and Rake.

See if one of them has a setting matching what is changed automatically: that would explain why your manual change is reversed.