This is in addition to SHiN's guide which is absolutely correct. The clock starts the moment the Prologue video starts and the clock stops when you either defeat Dracula the 2nd time OR you quit out to main menu.
It seems to me that if you hit the start button and sit in the game's menu, the clock STILL ticks!!
I had to go AFK for a bit so I hit the start button and parked on the in game menu, figuring that the clock would stop since I was not "playing" the game. Needless to say that this is NOT the case. I went AFK for about an hour and then finished up the game. To my surprise I didn't get the cheevo at the end of the credits. I looked at my final time and saw that it was 3:36:47. I knew for a fact that I finished the game around 2.5 hours.
IF you need to go AFK for any amount of time, just quit out to the main menu. The game saves an incredible amount of times (not on Hardcore) so you won't miss much, if anything by going to the main menu.
Please learn from my mistakes and current understanding of this finicky cheevo.