I have set up a second installation that I will use only for testing. It works, but with the same problem for custom labels. so version or database is not the problem. is there a package that I could be missing on the server maybe ?
Finally it seems to work 
- I was using my own invoice template across all groups, and generating a new custom template seems to take into account the custom labels.
It seems that custom labels are not updated when generating a new PDF, if the template predates the custom labels. I would suggest an improvement, because I do not think it could be a desired behavior.