Intellij IDEA 13 / Gradle - Trying to update build.gradle

Hi,

Everytime the project is refreshed, seems like IntelliJ IDEA 13 / Gradle is trying to update build.gradle. My build.gradle files are in SCM and is not checked out. So I see message asking to clear read-only status. 

1. What is it trying to add to build.gradle?
2. After I say 'ok' to clearing the read-only status, when I check the differences, there are no differences. So why is intellij asking me to change the read-only status or check out the file (after I configure the version control preferences)?

Similarly, in some cases, intellj 13 is asking to check out the gradle-wrapper.properties file (which is also in SCM).

Thanks

Anand