I'm in agreement with Tangofox.

When you apply vacuum directly from the pump, you apparently have enough flow to draw a vacuum at the shutoff diaphragm, despite the fact that the diaphragm is leaking.

However, when you go through the normal channels, via the ignition switch, the flow is probably reduced considerably due to restrictors and/or smaller tubing and a valve at the switch, so, when vacuum is applied to the shutoff diaphragm, it simply bleeds off and the engine cannot shut down.

If you cannot use a Mityvac to shut the engine down, it's time to replace the shutoff diaphragm on the IP.

And, make sure you read up on the proper procedure to change this diaphragm and, additionally, assume that you are going to do it incorrectly and the engine is going to run away. Make sure you are properly prepared.
Read up on this in the archives.