This seems to be occurring in Line 188 of ThrottleJobProperty.java:

                    if (/* not deleted */getItem(p.getParent(), p.getName()) == p && /* has not since been reconfigured */ p.getProperty(ThrottleJobProperty.class) == t) {
                        categoryProjects.add(p);
                        if (p instanceof MatrixProject && t.isThrottleMatrixConfigurations()) {
                            for (MatrixConfiguration mc : ((MatrixProject)p).getActiveConfigurations()) {
                                categoryProjects.add((AbstractProject<?,?>)mc);
                            }
                        }
                    }

getItem(p.getParent(), p.getName())

Is returning Null when the AbstractProject's parent is a Folder.

This looks a permission issue.
Steps to reproduce:

1. Launch Jenkins 1.642.1.
2. Install Cloudbees Folder 5.1
3. Install Throttle Concurrent Builds 1.8.4
4. Go to Manage Jenkins > Configure System, and add a new Multi-Project Throttle Category:
   • Category Name: category
   • Maximum Total Concurrent Builds: 0
   • Maximum Concurrent Builds Per Node: 1
5. Create a folder "folder"
6. Create a Freestyle project "test"
   • Check "Throttle Concurent Builds":
     • Check "Throttle this project as part of one or more categories"
     • Maximum Total Concurrent Builds: 0
     • Maximum Concurrent Builds Per Node: 1
     • Multi-Project Throttle Category: category
   • Check "Execute concurrent builds if necessary"
   • Add "Execute shell":

     sleep 10
     

7. Start a new build of "folder/test"
8. After the build started, start a new build of test again.
9. Result: test #2 doesn't start till #1 finish.
10. Go to Manage Jenkins > Configure Global Security and enable security.
    • Check "Enable security"
    • Check "Jenkins’ own user database"
      • Check "Allow users to sign up"
    • Check "Matrix-based security"
      • No permissions for Anonymous
      • All permissions for "admin"
11. Login as admin (signing up)
12. Start a new build of "folder/test"
13. After the build started, start a new build of test again.
14. Result: test #3 and test #4 runs at the same time (throttle-concurrent-builds doesn't work)

This is caused for throttle-cuncurrent-builds works as anonymous when it manages build queues,
and they can't access projects inside folders.
For projects outside folders, throttle-concurrent-builds can access them with a special method
provided by Jenkins core that doesn't perform permission checks.

Workaround: Add Overall/Read and Job/Read permissions to anonymous.

This is critical for me, and I'll work on this issue.

Created a pull request: https://github.com/jenkinsci/throttle-concurrent-builds-plugin/pull/35

Created a new pull request: https://github.com/jenkinsci/throttle-concurrent-builds-plugin/pull/37

Code changed in jenkins
User: ikedam
Path:
pom.xml
src/test/java/hudson/plugins/throttleconcurrents/ThrottleIntegrationTest.java
src/test/java/hudson/plugins/throttleconcurrents/ThrottleQueueTaskDispatcherTest.java
http://jenkins-ci.org/commit/throttle-concurrent-builds-plugin/d2f6ca409155c32dcb79d32c835614b95d9afc38
Log:
JENKINS-25326 Added a test to reproduce JENKINS-25326

Throttling doesn't work for projects in cloudbees-folder with Jenkins >= 1.536.

Code changed in jenkins
User: ikedam
Path:
src/main/java/hudson/plugins/throttleconcurrents/ThrottleQueueTaskDispatcher.java
http://jenkins-ci.org/commit/throttle-concurrent-builds-plugin/09234147a9bf23de0cd40cfa420cb8d4e97a4a6e
Log:
[FIXED JENKINS-25326] Elevates to SYSTEM when handling throttling in executor threads.

Code changed in jenkins
User: ikedam
Path:
pom.xml
src/test/java/hudson/plugins/throttleconcurrents/ThrottleIntegrationTest.java
http://jenkins-ci.org/commit/throttle-concurrent-builds-plugin/5b5728a069df14df1ce48377682b74ed338605df
Log:
JENKINS-25326 Reverted changes required for the test to reproduce JENKINS-25326.

Code changed in jenkins
User: Oleg Nenashev
Path:
pom.xml
src/test/java/hudson/plugins/throttleconcurrents/ThrottleIntegrationTest.java
http://jenkins-ci.org/commit/throttle-concurrent-builds-plugin/dfb3d2f13c139c430648556ece1f6b67d016dedb
Log:
JENKINS-25326 - Enable folder tests created by @ikedam

Code changed in jenkins
User: Oleg Nenashev
Path:
pom.xml
src/main/java/hudson/plugins/throttleconcurrents/ThrottleQueueTaskDispatcher.java
src/test/java/hudson/plugins/throttleconcurrents/ThrottleIntegrationTest.java
src/test/java/hudson/plugins/throttleconcurrents/ThrottleQueueTaskDispatcherTest.java
http://jenkins-ci.org/commit/throttle-concurrent-builds-plugin/c823d8d9284aa6d0e645b7c2a7702a4d1d354e2c
Log:
Merge pull request #41 from oleg-nenashev/feature/JENKINS-25326_ExecutorPermission

JENKINS-25326 - Elevate user to system during build throttling

Compare: https://github.com/jenkinsci/throttle-concurrent-builds-plugin/compare/e1aeb176b649...c823d8d9284a

Really sorry for accidentally updating this ticket! I hit a keyboard shortcut and must have pressed the wrong key because JIRA assigned the ticket to me. I've unassigned it again.