The NFC subsystem calls first onPause(), then onNewIntent() then onResume(). You should not need to work around this, since the whole process is very brief.
It seems the issue here is that your foreground mode is not activated. See the onCreate() method in DefaultNfcReaderActivity, and note the call to
setDetecting(true);
This is so because it is not necessarily so that you want to accept incoming NFC traffic at all times.