I've seen the same issue on a regular (non-Phonegap) iOS app with the 6.4.2 SDK (and earlier as well). When I get lucky enough to have it happen when I'm debugging, if I hit pause in Xcode, the main thread is hanging on a semaphore_wait_trap (often the main thread is doing core animation or something related to a webview when it hangs on the semaphore wait trap).
I've never had it happens when I have AdMob commented out (which I often turn off when I'm developing) so while I'm not 100% sure it's AdMob in my case it seems quite likely.
I'll continue to post updates here as I gather more information on this, however, I haven't found a reliable way to reproduce it yet.
-Todd