Issue with delayed inverval interruption having a timer Crystal installed

I have installed the timer Crystal (ABS06-107 and two 4pF caps) on several Pico's (v1.3 and v1.4b, firmware 2v19) for better time keeping. I'm already using this in two clocks and it's working fine for those applications.

I'm currently working on a 7 segment flip clock timer, which should start counting immediately after power is applied to the system.

The issue is that i'm experiencing a delayed interruption on the interval that is used to update the display. So with an interval of 1000ms, the 2nd second output to display is not executed.

In order to debug the issue, i've run the code below and used a scope to measure the output:

setInterval(function(){
digitalPulse(A5, 1, 10);
}, 50);

The results (see attached images) are that after an initial bootup of 7ms, the interval starts and runs for 1,5 seconds. Then the interval/output is interrupted for ~940ms and then continues (but slower and ramps up over the next half a second or so).

This interruption does not occur on Pico's without the Crystal, so i'm assuming this has something to do with initialising/changing the clock?
Is this correct (as in intended behaviour) and/or is there something to fix this with this setup (in firmware, or code or output pin (letting LED2 blink, has the same issue, so i don't think it's pin related))?

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