Installation Wizard: SEVERE errors in logs, enabling of the enabled plugin

It's a spin-off of JENKINS-34708. I'm experimenting with a custom Jenkins WAR file build. This build defines a custom update site, from which Jenkins takes plugins.

So the steps I perform:
1) Launch Jenkins with installation wizard
2) Go to the fine-grain select
3) Keep everything by default and press OK

Expected result:
1) Jenkins installs all plugins and starts up
2) No errors in the log

Actual result:
1) Jenkins installs the most of the plugins
2) Build timeout and matrix auth cannot be enabled according to logs
4) According to the filesystem, plugin.jpi.disabled files just do not exist at this time

The only useful info in the installation wizard is a stacktrace:

May 10, 2016 2:36:53 PM hudson.model.UpdateCenter$EnableJob run
SEVERE: Failed to enable Matrix Authorization Strategy Plugin
java.io.IOException: Failed to delete /Users/nenashev/Documents/XXX/tmp/plugins/matrix-auth.jpi.disabled
	at hudson.PluginWrapper.enable(PluginWrapper.java:444)
	at hudson.model.UpdateCenter$EnableJob.run(UpdateCenter.java:1447)
	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:511)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at hudson.remoting.AtmostOneThreadExecutor$Worker.run(AtmostOneThreadExecutor.java:110)
	at java.lang.Thread.run(Thread.java:745)