Sometimes the most basic things are the most important and easy to forget.
So when you need to do ST-PI or ST/A-PI upgrade ... its good to use little choice in upper menu :
Support package -> Import SPAM/SAINT Update
- then restart SPAM / SAINT
Its not written in SAP note when you are upgrading ST-PI or API .. because it's so easy, they suppose you know it.
Rest of process is in notes:
Note 539977 - ST-PI Support Packages