Hi Andy,
Are there any custom-built applications running on those particular Vista machines? It sounds like PTP is scanning and rescanning a file or application over and over again. (By default, PTP does not automatically document unknown processes. If it cannot find a reason to whitelist the process or alert on the process, it merely keeps rescanning it.)
Running the Sysinternals tool Process Monitor can reveal what file is consuming the CPU cycles in your instance. If that file is an application that you have developed yourself and you know it to be safe, I recommend adding it to the list of centralized exceptions. ("Add a Centralized Exception policy" in the SEPM....)
If the file is a .txt or .ini file or something similar, open it up and ensure that it is not corrupt/full of massive amount of repeated or garbage data. A corrupt file might also cause the behavior you are seeing. Delete or repair the file in question and the CPU spikes will cease.
One of those two answers is almost certainly your cause. Please keep the forum up-to-date with your progress!
Thanks and best regards,
Mick