It is two ways to check in files to vault from Inventor.
1. Right click in the vault browser check in files
2. Close model and answere yes in check in dialog box.
Problem.
If changing settings in option1 check in to " create visualisation files with job server" it is not changed in option 2 command. Then you need to do the same setting in both "check in" modes
Fix
Option 1 and 2 should link to same check in dialog box settings