The bug
Command block minecarts do not execute every tick but instead every 4 ticks. However, their cooldown is not saved to NBT. This means when a world with a command block minecart which is supposed to execute the next tick is closed, it will execute after 4 ticks again after the world is reopened.
How to reproduce
Summon a command block minecart
/summon command_block_minecart
Inspect its NBT data
/data get entity @e[type=command_block_minecart,limit=1,sort=nearest]
→ ❌ There is no tag tracking the execution cooldown
Can confirm that timers using command block minecarts fall progressively out of sync with other timers with each successive relog.