This is still happening in 1.6. with consequences.

Effectively, it makes it impossible to have several different builds in the same project root. Say you have

someProject

• build.gradle
• settings.gradle
• myBuild.gradle
• mySettings.gradle

And you execute gradle -bmyBuild.gradle --settings-file mySettings.gradle foo

You go once through :buildSrc with your custom settings, then again through :buildSrc with standard settings, then the build moves on to task foo from myBuild.gradle, but the custom settings where whacked by that second trip through :buildSrc

Try it with a mySettings.gradle that has something like this in it:

rootProject.setName('CustomRootProject')

Then put

task foo

as the only task in myBuild.gradle

Result:

:buildSrc:compileJava UP-TO-DATE
:buildSrc:compileGroovy UP-TO-DATE
:buildSrc:processResources UP-TO-DATE
:buildSrc:classes UP-TO-DATE
:buildSrc:jar UP-TO-DATE
:buildSrc:assemble UP-TO-DATE
:buildSrc:compileTestJava UP-TO-DATE
:buildSrc:compileTestGroovy UP-TO-DATE
:buildSrc:processTestResources UP-TO-DATE
:buildSrc:testClasses UP-TO-DATE
:buildSrc:test UP-TO-DATE
:buildSrc:check UP-TO-DATE
:buildSrc:build UP-TO-DATE
:buildSrc:compileJava UP-TO-DATE
:buildSrc:compileGroovy UP-TO-DATE
:buildSrc:processResources UP-TO-DATE
:buildSrc:classes UP-TO-DATE
:buildSrc:jar UP-TO-DATE
:buildSrc:assemble UP-TO-DATE
:buildSrc:compileTestJava UP-TO-DATE
:buildSrc:compileTestGroovy UP-TO-DATE
:buildSrc:processTestResources UP-TO-DATE
:buildSrc:testClasses UP-TO-DATE
:buildSrc:test UP-TO-DATE
:buildSrc:check UP-TO-DATE
:buildSrc:build UP-TO-DATE
----------------
someProject <============ SHOULD BE 'CustomRootProject'
I am foo
----------------
:foo UP-TO-DATE

BUILD SUCCESSFUL

As announced on the Gradle blog we are planning to completely migrate issues from JIRA to GitHub.

We intend to prioritize issues that are actionable and impactful while working more closely with the community. Many of our JIRA issues are inactionable or irrelevant. We would like to request your help to ensure we can appropriately prioritize JIRA issues you’ve contributed to.

Please confirm that you still advocate for your JIRA issue before December 10th, 2016 by:

• Checking that your issues contain requisite context, impact, behaviors, and examples as described in our published guidelines.
• Leave a comment on the JIRA issue or open a new GitHub issue confirming that the above is complete.

We look forward to collaborating with you more closely on GitHub. Thank you for your contribution to Gradle!

Thanks again for reporting this issue. We haven't heard back from you after our inquiry from November 15th. We are closing this issue now. Please create an issue on GitHub if you still feel passionate about getting it resolved.