Last entry overwritten with custom checkpoint key

[yozgoesdigital]

I noticed the last entry of each table is overwritten so making correction in the (target) database are lost. After a new entry is added things look persistent from the second last entry.
I have the feeling this happens since the checkpointing is done per table/tab in the 'Excel query file' and might have to do something with rounding of dates, I have looked at the code but I am not skilled enough to understand what really happens on the background.
Can someone confirm this behaviour?

commcare export tool: 1.2.1
database: Azure Sql server
Commcare export tool running in (K)ubuntu server.