"The whole conjecture was in response to a question about "why don't we see new phyla"?"
I think the answer is simply that we have too short a time frame (say a couple hundred years since people have really been looking - not enough time for anything to happen from an evolution point of view, except extinction).
The forams form one of the best cases for "punctuated equilibrium". There's a 10 million year stretch of great fossil data from the late miocene to the present.
(Malmgren, B.A., W.A. Berggren and G.P. Lohmann. 1983. Evidence for punctuated gradualism in the Late Neocene Globorotalia tumida lineage of Planktonic Foraminifera. Paleobiology 9:377-89.
Perhaps the fossil record doesn't reflect that these are the oldest creatures, but rather the deepest creatures. That would account for them being at the lowest levels.