when is your workflow firing? when someone loads it after the fact? when it's created?

it's triggered upon entry of the JE. First action is to set the approval status field to "pending approval"

I often build a separate scheduled workflow to auto approve the system generated noes that I don't want my users to have to touch.

@Roxane CdC there is a checkbox field in the transaction you can use as a condition named "Memorized" so you should be able to add, memorized = false or != true to exclude these from the process.