The allocations of commands in CommandQueueMT weren't aligned. This
commit aligns all accesses on 64bit boundaries regardless of target
platform. This ensures that all types are aligned.

Lock-wise the semaphores were maked as usable when the command had ran
but not when the synchronous stub had finished with it. This lead to a
race condition where sometimes the semaphore got reused before it was
waited on. We now mark the semaphore as free only once we're done
waiting on it.