Upsert not working for a bc over a custom table

 Hello,

we have created a totally custom table(hence it has no user key) and a bc over our custom table.

We have a wf that has an upsert step on the custom bc.

This wf is called from several stages of advancing an order(twice actually, once when order is submitted and once order is invoiced).

For the submit call upsert step inserts a new entry in our custom table.

For the invoiced call, upsert step should update the entry inserted on submit. 

But it does not always work like that, it sometimes inserts a new entry for the same order.