Subversion Tagging Plugin does not support running on matrix parents.
Even without Flexible Publisher plugin, your job should not run as expected.
Flexible Publisher plugin does not make a publisher who does not support matrix projects support them.

Anyway, Create a new ticket.

Jenkins LTS 1.532.1
Flexible publisher plugin 0.12
Jenkins Subversion Tagging Plugin 1.16

I have a matrix job with 2 labels and the flexible publisher as post build action.
I checked the check butten "Condition for matrix aggregation", set "Run on parent?" to "Always" and set "Perform subversion tagging on successful build" as action.

Result: The matrix parent job performs no tagging! The parent jobs console output even shows no output from the flexible publisher plugin.

Originally I hoped the new matrix support will solve this problem: https://issues.jenkins-ci.org/browse/JENKINS-9683

I added this feature in flexible-publish-0.11.
Please try, and report issues if something wrong.

Code changed in jenkins
User: ikedam
Path:
pom.xml
http://jenkins-ci.org/commit/flexible-publish-plugin/6b8fb4023efc2b50f456bd53f914ca95813db4ff
Log:
JENKINS-14494 Make compilable with JDK 1.7.

Code changed in jenkins
User: ikedam
Path:
src/main/java/org/jenkins_ci/plugins/flexible_publish/ConditionalPublisher.java
src/main/java/org/jenkins_ci/plugins/flexible_publish/FlexiblePublisher.java
http://jenkins-ci.org/commit/flexible-publish-plugin/4b03cee2f35acac2018237871495cb49897908ea
Log:
JENKINS-14494 Removed unnecessary imports.