Hi,
The plugin provides the list of shipment ids to MyParcel (it's MyParcel which generates the labels file, not the plugin) in the same order as displayed on the listing.
So if you don't get the labels in that same order, it means that the issue is on MyParcel's side.
One solution would be to request the labels separately and then fusion together the labels on your server, but that's really complex to do.
I think the first thing would be to contact MyParcel tech support on Slack to see what they have to say about this:
join.slack.com/t/myparcel-dev/shared_inv...wZDEyZDlhZTgzOWM1MjI