Clough42 - it may not be related, but there have been a few people who determined their heat bed would flex as the heater cycles on and off. That's the closest I remember anyone saying they see the Z axis changing with temperature. In those cases the varying Z-axis height led to print quality issues throughout the entire print, not just the beginning. Maybe in your case the Y-bed warms up with run time and keeps your heater flexed upwards.

Are you running with the same glass as before? Same clips and clips installed in the same place? Ambient room temperature about the same as before?