It all boils down to this: If and only if the kernel PPS code is
activated by ntpd FIRST, before anything tries to open the serial
port to actually read data, I am then able to start up gpsd (and by
extension the GPS reference clock) and have both GPS and PPS working
simultaneously.
However, if the serial port is captured by gpsd (and by extension the
GPS reference clock) FIRST, before the kernel PPS is activated,
kernel PPS fails and I get no PPS ticks.
I can imagine many possible reasons why it might not be workable in
your case...but if you connect the PPS line to one serial port and the
data lines to the other, you could use one port for PPS and the other
for GPS data with little to no chance of collision.
(Of course, it would be better to find and fix the real problem....)