Ok, I created a sample setup and was able to reproduce it like this:
1) git clone https://github.com/Hendrik-H/sample-gradle-init-plugin.git
2) cd sample-gradle-init-plugin
3) ./gradlew publisToMavenLocal
4) cd ..
5) git clone https://github.com/Hendrik-H/sample-gradle-distribution.git
6) cd sample-gradle-distribution
7) ./gradlew publisToMavenLocal
8) cd ..
9) git clone https://github.com/Hendrik-H/sample-gradle-project.git
10) cd sample-gradle-project
11) modify gradle/wrapper/gradle-wrapper.properties to point to local maven home (replace <home>)
12) ./gradlew dummy
-> output should show "***** Init Plugin is being applied *****" as the special gradle distribution with the init plugin is being used
-> the daemon for the sample distribution should be started now
13) cd ..
14) git clone https://github.com/Hendrik-H/sample-gradle-plugin.git
15) cd sample-gradle-plugin
16) ./gradlew clean build --info
-> my output contains "***** Init Plugin is being applied *****" below "sample.gradle.plugin.SamplePluginTest > testing sample plugin STANDARD_OUT"
which implies that the init plugin from the sample distribution got applied
17) ./gradlew --stop
18) ./gradlew clean build --info
-> This time "***** Init Plugin is being applied *****" is not in the output, so the init plugin was not applied
Let me know if there are further questions.