Version: 2.69 official release (Linux x64)
How to reproduce: Select bone, hit Ctrl + A > "Apply Visual Transform to Pose", watch as the bone goes somewhere other than the visual transform. Repeat the action and the bone again moves to a different place. This problem persists whether the bone has any active constraints or not; it only needs a non-zero starting point.
Expected behaviour: When "Apply Visual Transform to Pose" is applied to a constrained bone, that bone should remain in the same place when the constraint is turned to 0 (hence the term "visual" transform). If the bone has no constraints, nothing should happen. Instead, the bone gets moved all over the place in ways that don't make sense. If this is somehow intentional, I can't fathom how it could possibly be useful to the user.