Looks like we might have missed a 1.10 Patch
Link, for Alpha Protocol last week - although the fact that the .exe replacement from a few months back was also labelled v1.10 makes it confusing. This one actually lists some fixes and removes the copy protection. There are two versions - NA retail and "EU, Czech, Polish, Russian and Digital Download Versions", which seems an odd collection. According to a poster at Qt3, it seemed to work with his Steam version but I'd suggest caution.
* To resolve activation issues, PC copy protection has been removed.
* In Moscow during the assault of Brayko's Mansion, the player could get into a situation where a door would not be openable preventing progression through the rest of the level. This has been fixed.
* In Taipei, during the Stop the Assassination mission, the user can fall out of the world if they reload the "Exit Gardens" checkpoint. There was also a problem where if the player backtracked, part of the level might not load in properly. This has also been fixed.
* In the same mission, a problem with subtitles was corrected.
* In the museum in Rome, the game could crash when using Focused Aim to kill the NPC holding Madison in the elevator.
* Bosses could get stuck in an accelerated mode when Fury wears off.
* Chainshot was exploitable to slow time and get critical headshots without consuming its cooldown.
From RPGWatch