Any suggestions as to what might be going on?
With the default, the system could be locking on to any frequency divisible by 10. I haven't studied the circuit in detail. The OSC5A2B02 has a specified tuning of 1ppm/V so for a 1V change in the EFC you get a 10Hz change in the output. I'd say the 3.2V locked onto 10.00001MHz.
With a more frequent measurement the problem goes away (10 times a second, frequency divisible by 100 - apart from 10MHz the possibilities are outside the pulling range).
I think you are right.
I found the OSC5A2B02 datasheet was a bit unclear so I measured the tuning sensitivity myself using a Racal counter. It gives about 10Hz/Volt which agrees with the 1ppm/V figure you quoted.
Although the frequency counter I am using is not calibrated, it has an internal oven and 0.1Hz resolution. I 'think' it is reasonably accurate once the oven has stabilised.
When the loop is locked with 1PPS and a 3V tuning voltage, the OSC5A2B02 output frequency reads high by around 10Hz.
A tuning voltage of just under 2V gives 10.0000000 MHz on the counter.
So it appears that with a 1PPS timepulse, the loop is locking to 10.00001 MHz as you suggest.
I am trying to figure out a way to prevent this.
I may need to restrict the tuning range so that the loop is unable to pull the OCXO as far as 10Hz - although that may just prevent the loop from locking at all?
In the original article, he used an OCXO with a much lower tuning sensitivity (only 0.66Hz/V).
With a 5V supply than means it can only pull about +/- 1.6Hz max.
He suggests a simple potential divider could be used to reduce the tuning sensitivity (although his concern was the loop transient response rather than locking to the wrong frequency).
The problem with a potential divider is that the op amp that drives the tuning voltage will saturate at around 4V (It has a single 5V supply).
If the voltage is halved giving a tuning sensitivity of 5Hz/V, then it will struggle to reach the 2V required for 10MHz.
Maybe it needs something like a summing amp with variable gain and an adjustable dc offset?
An alternative is to find a solution to the timing pulse reverting back to the 1PPS default when the rechargeable lithium battery voltage drops if the unit is left unpowered for 2 weeks.
This could be the better solution because the loop works a lot faster with less droop when using a shorter pulse interval.