Dan,
I set mine up the same way, with the pcv going into the bottom of the air cleaner, and after about 60 miles I've got
oil on the valve cover with the breather. I'm guessing there is not as much vacuum thru the top of the carb, inside the filter, compared to under the carb. And as Trularin says, I have open ended baffles, and roller rockers, that don't help things. My Pro Systems carb has no vac port in the base, and I don't want to lean out a runner or two going into the intake, so a remote breather may be my solution.
Brad