Dear Heikki,
Thank you for the response.
Please be advised to raise this with our support team as it might need further investigation to narrow down the cause behind this behavior. You can reach support team at https://supportportal.gemalto.com/csm/ .
Kindly share the sample .apk file along with envelope project file (.prjx) with used protection settings to test.
To save project file :
1- Open envelope > "File" menu
2- "Save project as"
3- Save the .prjx file.
Best Regards,
Parth Kaushik