Looks like we both got crossed wires!
If you have a spare op amp you can use that to buffer the reference, the op amp will be subject to offset drift with temperature, if your not bothered about a couple of mV though its still useable, otherwise you could use an ultra low offset drift op amp like a Op07, or a chopper stabilised amp, they have silly low offset.
Thinking about it the output from the Gps is 1pps as you say, that might not be so great for the analogue ip of the 4046, too slow, you might need to put a schmitt trigger or transistor circuit between the Gps and the 4046 to square the signal up a bit, another thing with being slow is the 4046 will warm up as its input buffer wont like being operating in its linear region long.