I think this is related:
from patch 1.1 readme.rtf (found in root install folder), section Known Issues, Gameplay
- A very random input block might occur when using bombs, during dynamic fistfights, and with some interactions. If you encounter this issue, please load a previous game save.
It seems the input bug comes in varying degrees of seriousness and stubbornness.
Particularly when facing a boss later in the game there have been many reports of this bug happening so severely that nothing short of reloading works.